If you're not worried yet about the implications of trying terror suspects in a civil criminal court, maybe this will help:
The greatest danger posed in the trial of Khalid Sheikh Mohammed (KSM) isn't that he will go free. The greatest danger is that he will be convicted and that during his appeals the courts will ratify all of the extraordinary measures used to capture and convict him. The great danger is that the courts will ratify the rough, inaccurate and ambiguous norms of martial law as applying to all civil criminal trials.