Each option has its upsides and downsides.
Are we sure that they are all terrorists, or did Abu Gharib have car thieves, rapists, and credit card scammers?
A subdivision of letting them go would be to A) Hire some of them as informants B) Watch the others very closely
I suppose we could always plant a GPC chip in their left buttocks, with a miniscule particle of pig's blood, in case they decide to go suidice bomber on us. This chip could be removed after a probationary period of say 10 years or so. Of course this would literally cause the ACLU to foam at the mouth and double over with intestinal cramps, after which they would file so many complaints that our court systems would literally grind to a halt.