He used copyrighted software to create his website, and he did not know that doing so was haraam

It is not permissible to use tricks to download or copy
programs and discs whose authors have not given permission to download them
or copy them for free. That is because copyright is recognized. This has
been discussed previously in several answers, including the following: no.
95173, no.
72848, no.
102352. We have explained that
this is a general principle, but there may be exceptions to that in some
cases:

1 – If it is not available in the marketplace; in that case
it is permissible to copy it for personal use or charitable distribution,
and it is not to be sold or profited from.

2 – If there is a great need for it and the owners are
demanding more for it than it is worth, and they have already made enough
money to cover their costs with a reasonable amount of profit, and that is
something to be decided by experts. In that case it is permissible to copy
it for personal use, not with the aim of selling it.

3 – If these disks
belong to a company in a state that is at war against the Muslims, there is
nothing wrong with copying them, because those whose rights are to be
respected are: Muslims, non-Muslims living under Muslim rule, and
non-Muslims with whom the Muslims have a peace treaty – not non-Muslims who
are in a state of war against the Muslims. 

Based on that, if what you used comes under the heading of
one of these exceptions, then there is no blame on you. 

If that is not the case, then you have to ask Allah for
forgiveness and repent, and contact the authors of the program and ask for
their forgiveness. If they insist on the price of the program, then look at
the original copy and pay its price, and keep your website. 

And Allah knows best.