Expert opinion over at Nat. Review on-line suggests that the court supported the first interpretation--that we can keep them as long as the conflict is going on.
So long as SCOTUS doesn't hold in the future that the GITMO detainees are entitled to due process in Americas courts this is the best of all worlds. The WOT isn't gonna end in their life times. And now they can be held for the duration without all the yapping about their day in court.
Of course, I'm dreaming. There may well be 5 votes on SCOTUS to usurp the CIC's war making authority. Sad but true.