I agree with you that Congress must set up some sort of guidelines specifically tailored to dealing with terrorist suspects, though, I'm not sure I'd make them quite as strict as you suggest... but anyway, I have a different point.
If Congress did try to pass some form of legislation (which I also find unlikely in a Republican controlled Congress), surely the administration would try to get such a law declared unconstitutional. After all, it seems that the administrations's case in the Padilla and Hamdi matters are based on what Ted Olson says are the President's inherent constitutional authority as commander-in-chief. Hopefully, they would lose such a case, but that remains to be seen.
If the executive continues to claim this kind of unfettered power, what kind of power does Congress have to stop them? You quote Gonzalez saying that people "may be detained for the duration of hostilities." Who gets to say how long the hostilities last? The Prez, I'm sure. Because Congress never declared war.
Don't get me wrong, I would love to see a power struggle between Congress and the President, I just don't think it's going to happen.