Let's see, we could just kill them. Wait...
"...many CIA officers believed that the al Qaeda leaders would be worth keeping alive to interrogate about their network and other plots. Some officers worried that the CIA would not be very adept at assassination.
'We'd probably shoot ourselves," another former senior CIA official said.'"
OK, let's ship 'em off to other governments who will torture them. Check.
Oh, wait - we're getting flak over that? Alright, let's just set up some secret dungeons of our own in, I don't know... Eastern Europe?