Holder's evasiveness in answering the question is interesting, because the answer seems fairly obvious. Whatever goes on while the prisoner is in military custody is not part of the judicial process and interrogation there is clearly for purposes of intelligence and not admissible in court. All of that would change once he was transferred to civilian custody, at which point he would be read his rights and given a lawyer and interrogated just like any other suspect.
The dividing line between military custody and civilian custody seems absolutely clear-cut. So why was it so difficult for Holder to acknowledge it and admit that the cost of bringing terrorists to trial in civilian courts is giving them rights and protections they would not have in military custody? Doing this is hardly going to destroy his case against the terrorists. All of the physical evidence would still be admissible as would witness testimony. The only thing they would have to give up would be any confessions, and since those may have been obtained under duress they wouldn't be admissible under any circumstances anyway.
Some who have examined the peculiar circumstances raised by the plans to try these terrorists in New York have raised questions about the lengthy incarceration in military custody being a violation of the right to a speedy trial, and issues of cruel and unusual punishment relating to interrogation techniques. These questions are actually largely irrelevant. Holder could make them all go away if he had the strength to draw that clear line between military custody and civilian custody and effectively say "what happens in GITMO stays in GITMO" and build his case on the ample, legitimate evidence against these terrorists.
Clearly the rules and standards are different when you are a military prisoner and when you are a criminal indicted for trial in a civilian court. People understand this. Why can't Holder explain it? Lindsey Graham gave him a perfect opportunity to draw that line clearly and Holder just couldn't bring himself to give a straight answer. Instead he gave the impression that he and the administration have no idea what they're doing with these terrorists and haven't thought their policy through at all, even when sensible answers ought to be simple to come up with.