Seems to me that the problem here is whether or not Congress has any authority to determine what constitutes an enemy combatant…the term may be employed to appease some individuals but an act of treason against the United States which involves a direct and immediate threat would fall under the Commander-in-Chief's authority to apprehend and bring to justice.
If it's learned you have foreign agents conducting operations to bring down the federal government, the president may apprehend these individuals and try them in military court as part of the fundamental law inherent in the President's office, namely, his obligation to protect the states from foreign intrusion. We would not, for example, claim that before the President could apprehend armed soldiers crossing the border from Canada, that an act of Congress would be required…the situation with a foreign intrusion would be the same.
It does not require acknowledgement from Congress or clarification on what constitutes a foreign intrusion. It's an entirely different jurisdiction altogether…Congress passes laws under Article I section 8 but that does not mean that such body of law is the only law in existence. Even if Congress has passed no laws…the President maintains Article II authority. The Enemy Combatant argument, then, may be the wrong road to go down for the white hats, because the Military Commissions Act is actually pulling pure, fundamental Article II authority under Article I and renders the President's authority to protect and defend the Constitution subject to Congressional review. It's pulling the law of war down and turning it into a function of Congressional act where it has no place.
This may seem a frightening interpretation…it is to me…but can POTUS stand firm on his rightful Constitutional authority here? The minute someone is declared an enemy combatant, seems to me that Congress is brought into the picture, which is fine for lower offenders, but not for the higher ones.