Personally, if I knew that a bunch of limp wrists would cause problems with the detainment and treatment of terrorists, then I would keep captured enemies in a different country, the ones worth keeping at least. Those not worth keeping would be shot where they were caught or after an initial interrogation.
This is war people, and for those of you who can't stomach it, too bad. Let the men who know how to conduct warfare do their jobs. If you want to stand up with the enemy and defend them, then you become the enemy.