The problem is that you need to take prisoners to get the Intel. Kill everybody & you learn nothing. The Supremes have made it difficult because a civilian trial will require the Pentagon to bring classified material into the courtroom. I suspect that the prosecution will just release most of these detainees rather than reveal what they have on them in open court.
OTOH, we will be treated to circus trials for the baddest-of-the-bad. (And some may go free.) Either way, America loses.
I have a feeling our allied Iraqi and Afghan troops will be doing most of the prisoner-taking and interrogating from here on out.