In large part I don't. During the Cold War we managed to try any number of spies using the civilian court system. We have tried and convicted many terrorists using the civilian court system. We did so and won the Cold War without establishing a dictatorship where the executive gathers evidence, evaluates it own its own, imposes it own sentence, and carries it out on its own. The stuff about the incapacities of civilian courts is nonsense and you have to be distrustful of any public official who makes that claim. It's the dog-ate-my-homework of jurisprudence.
we tried those cold war spies post-facto their actual crimes. Padilla didn't commit a terrorist act, he was involved in a conspiracy to do so. the evidence against him doesn't involve the actual act itself, we got him before he could commit it.
just imagine the ACLU deposition of Khallid Sheik Mohammed at Padilla's trial. the first words out of his mouth would be "the CIA tortured me". what happens next, does the defense get to call those CIA officers to the stand to ask them about that?