As a matter of domestic law, Congress can overrule treaties by subsequent enactment. But, as a matter of international law, the US would be in breach of its treaty obligations if they did so.
It might be good domestic politics to stick it to the Court. No doubt Breyer's concurrence will be quoted. But the rest of the West is not going to take well to this.
On Wednesday, Guantanamo was already a problem for Tony Blair and for other pro-US Western politicians. But it could at least be argued that the Geneva Conventions do not apply to captured purported al Qaeda members.
Not any more.
Because this is a matter of the US's treaty obligations to all the other signatories of the Geneva Conventions, it becomes an issue of the politics of each of those other countries. The Khadrs are Canadian citizens in Guantanamo -- clearly, the Canadian government has to consider its diplomatic position. The Canadian courts, and the European courts, are sure to get involved.
Update: Carlos Vázquez, who authored one of the amicus briefs on the application of the Geneva Convention, makes the point better here.