Following the lead of the New York Times, which had a similar story (11/2/08) right before the election, Newsweek's Dan Ephron has a piece (11/7/08) on "The Gitmo Dilemma," explaining why Obama "won't close the controversial prison soon."
Like the Times story, Newsweek struggles to complicate a simple situation. The U.S. had three things it could do with prisoners that were in accord with international law and the U.S. Constitution: It could have released them; it could put them on trial in civilian court; or it could have treated them as prisoners of war with the protection of the Geneva Conventions.
It was only the Bush administration's determination to preserve the ability to torture the prisoners that necessitated their placement in Guantanamo–which the administration hoped would be treated as a Constitution-free zone–and the creation of a parallel justice system where defendants' legal rights would be limited.
The fact that Guantanamo was used for its intended purpose of abusing prisoners makes it difficult if not impossible at this point to give them real trials. But they can presumably still be treated as POWs, as long as a legitimate tribunal determines them to be combatants in an ongoing conflict. Contrary to what Newsweek and the New York Times say, constructing a prisoner of war camp for a few dozen prisoners would not be at all beyond the capabilities of the U.S. military.
See FAIR's magazine Extra!: "Take No Prisoners: U.S. Reporters Failed to Probe Pentagon's 'Unlawful Combatants' Label" (3-4/02) by Steve Rendall