I see nothing suggesting that Padilla isn't guilty as h*ll, but suppose he isn't? Will he ever get a chance to prove it before this endless undeclared "War on Terrorism" comes to a close (ha, ha)? You think that you could not be framed into such a Kafkaesque trap?
I'll turn that around. Suppose he IS, and through the civilian court system, he gets set free to blow up tens of thousands. Then, where would you stand? Is it better to protect the many or worry about the one? Now, this philosophical arguement does bring up important constitutional questions and the Supreme Court will NO DOUBT be the final arbitrar of that case. Until then, we can argue all day and it changes nothing.
For me, it's a question of protecting the many (women, and innocent children- and Bubbas like you and me) or protecting the due process of what is more than likely a terrorist hellbent on destroying you and all of your freedoms.