Federal Legislation is not \"nullified\" by GATT or any other treaty
I think you likely misread the Supreme Court's opinion. It did not rule that the Geneva Convention over-rode a conflicting Act of Congress which had been signed into law. Rather, the President could not do "X" because there was no basis in Federal law to rely on. Congress had not authorized what the President was doing.
Justice Stephen Breyer in a concurrence wrote, "The Court's conclusion ultimately rests upon a single ground: Congress has not issued the Executive a 'blank check.'"
The Washington Post also reported it differently than you recall it, noting that there was no basis in US Federal law for the detention regulations being challenged:
"Brushing aside administration pleas not to second-guess the commander in chief during wartime, a five-justice majority ruled that the commissions, which were outlined by Bush in a military order on Nov. 13, 2001, were neither authorized by federal law nor required by military necessity, and ran afoul of the Geneva Conventions.
Detainees at Guantanamo Bay, Cuba, must have courts-martial, the Supreme Court ruled, or the president can ask for legislation to proceed differently. (Pool Photo By Brennan Linsley)
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As a result, no military commission can try Salim Ahmed Hamdan, the former aide to Osama bin Laden whose case was before the justices, or anyone else, unless the president does one of two things he has resisted doing for more than four years: operate the commissions by the rules of regular military courts-martial, or ask Congress for specific permission to proceed differently"
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