We do in fact allow the courts to decide as that is their constitutional job to decide all cases in law and equity. As for the second part, this is why we have investigators and prosecutors who build cases when they suspect people of committing crimes instead of simply shutting down communications when they suspect someone is doing something wrong.
wars, and the handling of agents of foreign powers - are different. that's the whole argument here. interment of japanese americans was "unconstitutional" by civilian standards, but at the time was appropriate.
anyway, your are going to get your wish. the enemy combatant designation will be eliminated. the dirty bomb charges against Padilla will never see the light of day, hopefully he can be convicted of these lesser charges, otherwise he will walk.
and this is going to go on and on - the SCOTUS will also extend US rights to non-citizens held overseas (like they did at Gitmo), perhaps ordering the CIA produce the top AQ suspects they are holidng for their "due process" rights. we'll see what you have to say whem that happens - I guess you will be for it, you seem to feel the courts are "infallible".