He was junub and the iqaamah for prayer was given – should he pray or do ghusl even if he will miss the prayer in congregation?

The person who is junub must do ghusl in order to pray, and
his prayer is not valid without it, because Allaah says (interpretation of
the meaning): 

“O you who believe! Approach not As‑Salaah (the prayer)
when you are in a drunken state until you know (the meaning) of what you
utter, nor when you are in a state of Janaaba (i.e. in a state of sexual
impurity and have not yet taken a bath), except when travelling on the road
(without enough water, or just passing through a mosque), till you wash your
whole body”

[al-Nisa’ 4:43].

And the Prophet (peace and blessings of Allaah be upon
him) said: “No prayer is accepted without purification.” Narrated by Muslim
(224). 

This is a matter upon which there is scholarly consensus. 

Al-Nawawi (may Allaah have mercy on him) said: The Muslims
are unanimously agreed that prayer is haraam for the one who is impure, and
they are unanimously agreed that prayer is not valid if he does it, whether
he knows that he is impure or he was unaware of it or forgot it. But if he
prays out of ignorance or because he forgot, there is no sin on him. If he
knew of the impurity and the prohibition on praying when impure, then he
committed a grave sin, but in our view he does not commit kufr thereby
unless he regarded that as permissible. But Abu Haneefah said: He does
commit kufr because he took the matter lightly. 

Conclusion: it is a sin, do it is like zina and other sins.
That is if he was forced to pray when impure. End quote from al-Majmoo’
(2/78). 

The one who is junub must do ghusl first, then pray, even if
doing ghusl means that he will miss the prayer in congregation. 

See also question no. 94311. 

And Allaah knows best.