It means that "commander in chief" doesn't trump "supreme law of the land" which international treaties are presumed to be.
The problem here is what constitutes "these sorts of things". They've merely restricted the form under which this handful of prisoners may be tried. It isn't like they said he had to be released tomorrow, or that Gitmo was unconstitutional.
So under what form will they be tried? In U.S. Courts? That's a different way to handle a war.