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The problem with your argument is that the Protocols are international treaties that our Senate have not ratified. Thus, we are not a direct party to them and, therefore, they certainly have no force of law within the US.You cannot expect the USSC to base its decisions on international law that, by our Constitution, is not binding on us.
Except that the U.S. Constitution says (Article VI)
...and all Treaties made, or which shall be made, under the Authority of the United States, shall be the supreme Law of the Land;...
And the Vienna Convention on the Law of Treaties says, (Article 14)
1. The consent of a State to be bound by a treaty is expressed by ratification when:
...(c) the representative of the State has signed the treaty subject to ratification;
Are you going to argue that the President of the United States does not have the power to sign treaties subject to ratification?
Why do you think the Bush administration withdrew their signature from the Rome Statute during the scramble to try to make torture legal for Abu Zubaydah in 2002?
The point is moot anyway, the validity of Geneva in all armed conflict requires at least Article 3 protections, and requires an Article 5 hearing (not a presidential decree, regardless of any "Article II powers") in order to reduce the requirements to Article 3. If there were an argument that al Qaeda must be treated as international criminals because there is no war, that's one thing. Then they cannot be held "for the duration of conflict" because there is no conflict. But if they are to be treated as adversaries in war, you can't wriggle the U.S. out of the Geneva Conventions.
Oddly, this situation is profoundly confused in Afghanistan right now, since the U.S. has prisoners under control of the U.S. military, but technically there was a cessation of conflict a long time ago, and the U.S. maintains that there is no occupation, either. Technically the U.S. military has no jurisdiction to hold prisoners there. Want to talk about extradition without hearings from Pakistan and Afghanistan? Eric Holder has a frigging mess on his hands to restore all this lawlessness to the rule of law, and will need help from the military lawyers as much as the civilian lawyers.
As I've mentioned before here, perhaps the Afghan government can help, since they can request investigation and prosecution from the International Criminal Court. The U.S. is not a signatory, but they don't have to be for the court to issue arrest warrants against anyone who committed war crimes in an acceding or signing state, and Afghanistan acceded in February 2003. Maybe Carolyn Woods can plea bargain for a lighter sentence with information incriminating the top of our current government. Bush will then be the rough equal of Omar al Bashir.