The fact that the Prophet (blessings and peace of Allah be upon him) pardoned ‘Abdullah ibn Abi Sarh does not mean that the hadd punishment for apostasy was waived

Perhaps the hadith referred to in the question is that which was narrated by
Sa‘d ibn Abi Waqqaas (may Allah be pleased with him), who said: On the day
of the Conquest of Makkah, ‘Abdullah ibn Sa‘d ibn Abi Sarh hid with ‘Uthmaan
ibn ‘Affaan, who brought him to the Prophet (blessings and peace of Allah be
upon him) and said: O Messenger of Allah, accept the allegiance of
‘Abdullah. He raised his head and looked at him three times, and refused
each time, then he accepted his allegiance after three times. Then he turned
to his companions and said: “Was there no wise man among you who could have
stood up when he saw me holding back my hand from (accepting) his
allegiance, and killed him?” They said: We did not know, O Messenger of
Allah, what was on your mind. Why didn’t you make some hint to us with your
eyes? He said: “It is not appropriate for a Prophet to deceive with his
eyes.” 

Narrated by Abu Dawood (4359) with a saheeh isnaad; classed as saheeh by Ibn
Taymiyah in as-Saarim al-Maslool (2/219); Ibn Mulqin in al-Badr
al-Muneer (7/450); Ibn Hajar in at-Talkhees al-Habeer (3/1136);
al-Albaani in as-Silsilah as-Saheehah (4/301) 

If
this hadith is the one referred to, there is nothing in it to indicate that
the apostate is not to be executed. ‘Abdullah ibn Sa‘d ibn Abi Sarh deserved
to be executed for two reasons: 

1. Because he had
apostatised from Islam and had gone back to disbelief after having been
guided.

Execution for this reason is the right of Allah, may He be exalted, but is
waived if the apostate repents and comes back to Islam. 

2.Because he used to
revile the Messenger of Allah (blessings and peace of Allah be upon him) and
fabricate lies against him by saying that the Messenger of Allah (blessings
and peace of Allah be upon him) used to change things in the Qur’an
according to what Ibn Abi Sarh dictated to him.

This was narrated by Ibn Ishaaq in as-Siyar wa’l-Maghaazi. And it was
narrated from Abu ‘Ubaydah ibn Muhammad ibn ‘Ammaar ibn Yaasir and ‘Abdullah
ibn Abi Bakr ibn Hazm that he only issued instructions that Ibn Abi Sarh
should be executed because he had become Muslim, and he used to write down
revelation for the Messenger of Allah (blessings and peace of Allah be upon
him), then he went back to shirk and joined the people of Makkah, and he
used to tell them: “I used to direct him however I wished; he used to tell
me to write something for him, and I would say to him, ‘or such and such, or
such and such,’ and he would say: ‘Yes.’” That was because the Messenger of
Allah (blessings and peace of Allah be upon him) used to say “ ‘Aleem
Haleem (All-Knowing, Most Forbearing)” and he would say to him, “Or I
will write ‘Azeez Hakeem (Almighty, Most Wise), and the Messenger of
Allah (blessings and peace of Allah be upon him) would say to him: They are
both the same. 

End quote from as-Saarim al-Maslool (p. 111) 

Ibn Ishaaq also said: 

 One of our scholars told me that Ibn Abi Sarh went back to Quraysh and
said: By Allah, if I wished I could say something like what Muhammad says,
and I could bring something like what he brings. He would say something and
I would change it to something else, and he would say: You are right. Then
Allah, may He be exalted, revealed concerning him the words (interpretation
of the meaning): “And who can be more unjust than he who invents a lie
against Allah, or says: “I have received inspiration,” whereas he is not
inspired in anything” [al-An‘aam 6:93]. For this reason the Messenger of
Allah (blessings and peace of Allah be upon him) issued orders that he was
to be executed.

It
was narrated that Ibn Abi Nujayh said: The Messenger of Allah (blessings and
peace of Allah be upon him) only issued orders that he be executed because
he had become Muslim, and he used to write down the revelation for the
Messenger of Allah (blessings and peace of Allah be upon him). Then he
apostatised and returned to shirk, and he went back to Quraysh and said: “By
Allah, I used to direct him however I wished; he used to tell me to write
something for him, and I would say, ‘or such and such, or such and such,’
and he would say: ‘Yes.’” That was because the Messenger of Allah (blessings
and peace of Allah be upon him) used to dictate to him and say ‘Azeez Hakeem
(Almighty, Most Wise) or Hakeem Haleem (Most Wise, Most Forbearing) and he
would write one of the two and he would say: They are both correct.

End quote from as-Saarim al-Maslool (p. 112) 

Execution for this reason was the prerogative of the Prophet (blessings and
peace of Allah be upon him) and could be waived by his pardon. 

The most that may be said about what happened in this incident is:

The first reason was waived because of the repentance of ‘Abdullah ibn Abi
Sarh and his return to Islam; in fact he became a good Muslim after that.
The one who repents from apostasy is not to be subjected to the hadd
punishment, according to the more correct of the two scholarly views. 

The second reason was waived because of the pardon of the Prophet (blessings
and peace of Allah be upon him), after the intercession of ‘Uthmaan ibn
‘Affaan (may Allah be pleased with him). 

The evidence that Ibn Abi Sarh repented is seen in a number of things, as
follows: 

-1-

‘Uthmaan ibn ‘Affaan (may Allah be pleased with him) addressed the Prophet
(blessings and peace of Allah be upon him) according to this report by
saying: “Accept the allegiance of ‘Abdullah.” On what basis could allegiance
have been sworn except on the basis of Islam, truth and good?

 -2-

Other reports clearly mention repentance, such as the report narrated in
al-Maghaazi (2/855) by al-Waaqidi, in which it says: He fled from
Madinah to Makkah as an apostate, and the Messenger of Allah (blessings and
peace of Allah be upon him) issued instructions that he be executed on the
day of the conquest of Makkah. On that day, Ibn Abi Sarh came to ‘Uthmaan
ibn ‘Affaan (may Allah be pleased with him), who was his brother through
breastfeeding, and said: O my brother, I have chosen to come to you, so keep
me here, and go to Muhammad and speak to him concerning me, for if Muhammad
sees me, he will strike me in the face, for my crime is the greatest of
crimes, but I have come repenting. 

-3-

The views of the scholars who wrote the biography of ‘Abdullah ibn Abi Sarh
are all unanimously agreed that he became Muslim on that day, and became a
good Muslim after that. 

Al-Baghawi narrated in Mu‘jam as-Sahaabah (4/24, 250), with his
isnaad going back to Yazeed ibn Abi Habeeb who said: When ‘Abdullah ibn Sa‘d
ibn Abi Sarh was dying: when he was in ar-Ramlah, where he had fled from
turmoil, he kept saying to them all night: Has morning come? And they would
say: No. Then when morning came, he said: I feel the coolness of the
morning, go and look, then he said: O Allah, make my final deed Fajr prayer.
So he did wudoo’, then prayed. In the first rak‘ah he recited al-Fatihah and
al-‘Aadiyaat (surah 100), and in the second rak‘ah he recited al-Faatihah
and another surah. Then he said the tasleem to his right, and he went to say
the tasleem to his left, but Allah, may He be glorified and exalted, took
his soul. 

Ibn ‘Abd al-Barr (may Allah have mercy on him) said: 

‘Abdullah ibn Sa‘d ibn Abi’s-Sarh became Muslim during the conquest of
Makkah, and he became a good Muslim, and he did not do anything to be
criticised for after that.

End quote from al-Isti‘aab fi Ma‘rifat al-Ashaab (3/918) 

An-Nawawi (may Allah have mercy on him) said: 

Then on that day ‘Abdullah ibn Sa‘d ibn Abi Sarh became Muslim, and he
became a good Muslim; after that he did not do anything to be criticised
for. He was one of the wise and noble men of Quraysh. ‘Uthmaan appointed him
as governor of Egypt in 25 AH, and Allah granted the conquest of North
Africa at his hands, which was a great conquest in which the share of a
horseman was three thousand mithqaals of gold. Also present with him during
this conquest were ‘Abdullah ibn ‘Umar, ‘Abdullah ibn ‘Amr ibn al-‘Aas, and
‘Abdullah ibn az-Zubayr. This ‘Abdullah ibn Sa‘d was a horseman of Banu
‘Aamir ibn Lu’ayy. After the conquest of North Africa, he waged a campaign
against the blacks of Nubia in 31 AH, and he fought the campaign of as-Sawaari
by sea against the Byzantines. 

When ‘Uthmaan ibn ‘Affaan was killed, ‘Abdullah ibn Sa‘d ibn Abi Sarh
withdrew from the turmoil and stayed in Asqallaan (Ashkelon) – or, it was
said, in ar-Ramlah. He prayed to Allah to end his life in prayer, so he said
the first tasleem at the end of Fajr prayer, then he wanted to say the
second tasleem on his left, (and died). He died in 36 AH.

End quote from Tahdheeb al-Asma’ wa’l-Lughaat (1/270) 

One of the following two reasons would have been sufficient to execute
‘Abdullah ibn Sa‘d ibn Abi Sarh: 

If
he had apostatised and had not told lies about the Prophet (blessings and
peace of Allah be upon him), that would have incurred the penalty of
execution, but repentance wards off that hadd punishment. 

If
he had reviled the Prophet (blessings and peace of Allah be upon him) and
fabricated lies against him, that would also have incurred the penalty of
execution, and the hadd punishment would not have been waived in this case
except by a special pardon from the one who was wronged, namely the Prophet
(blessings and peace of Allah be upon him). As he pardoned him, the hadd
punishment was waived from him, i.e., the hadd punishment for offending the
Prophet (blessings and peace of Allah be upon him) and fabricating lies
against him and about the revelation. This did not apply to the hadd
punishment for recanting Islam and going back to idol-worship; his
repentance was sufficient to waive that punishment. 

Shaykh al-Islam Ibn Taymiyah (may Allah have mercy on him) said: 

‘Abdullah ibn Sa‘d ibn Abi Sarh apostatised and fabricated lies against the
Prophet (blessings and peace of Allah be upon him), saying that he used to
dictate the revelation to him and he would write for him whatever he wanted.
The Prophet (blessings and peace of Allah be upon him) issued instructions
that he was to be executed, and one of the Muslim men vowed that he would
surely kill him. Then ‘Uthmaan kept him in his house for several days until
the people of Makkah felt safe, then he came as a penitent to swear
allegiance to the Prophet (blessings and peace of Allah be upon him) and ask
him to grant him safety. The Messenger of Allah (blessings and peace of
Allah be upon him) remained silent and did not answer him for a long time,
hoping that the one who had made that vow or someone else would get up and
kill him, and fulfil his vow. 

This indicates that the one who fabricates lies against the Prophet
(blessings and peace of Allah be upon him) and impugns him may be executed
and his blood is permissible to be shed, even if he comes repenting from his
disbelief and fabrications, because if killing him were haraam, the Prophet
(blessings and peace of Allah be upon him) would not have said what he said,
and he would not have said to the man: “Why did you not fulfil your vow to
kill him?” 

There is no difference of opinion among the Muslims as far as we know
concerning the fact that if a disbeliever comes repenting and wanting to
become Muslim, expressing that openly, it is not permissible to kill him for
that. In that regard there is no differentiation between one who was
originally a disbeliever and one who apostatised. 

In
fact, if a disbeliever comes wanting to learn about Islam and to hear the
Qur’an read to him, it is obligatory to grant him safety for that purpose.
Allah, may He be exalted, says (interpretation of the meaning):

“And if
anyone of the Mushrikoon (polytheists, idolaters, pagans, disbelievers in
the Oneness of Allah) seeks your protection then grant him protection, so
that he may hear the Word of Allah (the Quran), and then escort him to where
he can be secure”

[at-Tawbah 9:6]

And Allah, may He be exalted, said concerning the mushrikeen (interpretation
of the meaning):

“But if they repent and perform As-Salat (Iqamat-as-Salat),
and give Zakat, then leave their way free”

[at-Tawbah 9:5]. 

‘Abdullah ibn Sa‘d only came repenting and promising to establish prayer and
give zakaah; in fact he came after he had become Muslim. 

Moreover, the Prophet (blessings and peace of Allah be upon him) was hoping
that he would be killed, and he said to the people, “Why didn’t some of you
get up and kill him?” and “Why did you not fulfil your vow to kill him?”
Thus it is known that it was permissible for him to kill those among the
disbelievers who fabricated lies against him and offended him, even if they
came showing that they wanted become Muslim and repent after the Muslims
gained power over them. 

This clearly indicates that fabricating lies against him and offending him
makes it permissible to execute the one who does that, even if he outwardly
appears to be a Muslim and to have repented.

End quote from as-Saarim al-Maslool (408-409). 

He
(may Allah have mercy on him) also said: 

When ‘Abdullah ibn Sa‘d ibn Abi Sarh impugned him and fabricated lies
against him, to undermine him, after he had become Muslim, the Prophet
(blessings and peace of Allah be upon him) issued orders that he be
executed, and refused to accept his oath of allegiance. We have seen above
the evidence which confirms that the one who insults the Prophet (blessings
and peace of Allah be upon him) may be executed even if he becomes Muslim,
and we stated that he came to him as a Muslim and repentant. He had become
Muslim before he came to him, as we have narrated from more than one
narrator, or he came wanting to become Muslim. The Prophet (blessings and
peace of Allah be upon him) knew that he had come wanting to become Muslim,
then he refrained from responding to him, waiting for a man to get up and
kill him. 

This indicates that in the case of someone like this apostate who had
insulted the Prophet (blessings and peace of Allah be upon him) it is not
obligatory to accept his repentance; rather it is permissible to kill him
even if he comes repenting. We have stated that in the past and here in
several ways. What protected a person’s life was the pardon of the Messenger
of Allah (blessings and peace of Allah be upon him), not merely the fact
that he had become Muslim. Becoming Muslim and repenting erase sin, but the
pardon of the Messenger of Allah (blessings and peace of Allah be upon him)
protected his life. This pardon ended with the death of the Prophet
(blessings and peace of Allah be upon him), and the ummah does not have the
right to pardon anyone on his behalf. The fact that he refused to accept his
oath of allegiance until someone got up and killed him indicates that it is
permissible to execute him, even if he comes repenting.

End quote from as-Saarim al-Maslool ‘ala Shaatim ar-Rasool (p. 340) 

For more information on the hadd punishment of the apostate, please see the
following fatwas: 12406, 14231,
20060, 20327,
142522 

To
sum up: this hadith does not show that the hadd punishment for apostatising
from Islam to disbelief has been waived; rather what was waived (in this
case) was the hadd punishment for fabricating lies against the Prophet
(blessings and peace of Allah be upon him), and there is a great difference
between the two matters. 

And Allah knows best.