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.
After a couple of decades of these court decisions reverberating throughout the legal system, we could end up living under de facto martial law.
[. . .]
For over two hundred years we were careful to keep a firewall between civil and martial law. We did so because civil and martial law are polar opposites. Civil law is focused on protecting the rights of the accused against the overwhelming power of the state. When there is doubt, the accused walks free. Martial law is focused on imposing a minimal order on bloody chaos. It was focused on allowing the military to complete its mission and win wars. When there is doubt, the accused is presumed guilty.
Now, Obama wants to bring martial law into a civil court room in Manhattan. In order to let a civil conviction of KSM stand, the higher courts will have to overturn almost all the current constitutional protections of the accused.
[. . .]
As the author notes, "Nothing good will come of this trial" and the biggest danger is not that