'Mr. Obama issued a statement calling the decision “a rejection of the Bush administration’s attempt to create a legal black hole at Guantánamo” that he said was “yet another failed policy supported by John McCain.”
“This is an important step,” he said of the ruling, “toward re-establishing our credibility as a nation committed to the rule of law, and rejecting a false choice between fighting terrorism and respecting habeas corpus. Our courts have employed habeas corpus with rigor and fairness for more than two centuries, and we must continue to do so as we defend the freedom that violent extremists seek to destroy.” '
Prof John Yoo in his excellent book 'War By Other Means' lays out a throughly researched argument as to why the Supreme Court should stay out of the war or terror.
His point is that those in Gitmo are enemy combatants and are not prisoners of war. To be a POW the warring nations must have accepted the Geneva Conventions and follow the rules of war. Most terrorist organizations are not linked to nation states and thus are not signatories of the Geneva Conventions. The Taliban in Afghanistan are not signatories to the Geneva Conventions and therefore those captured in that theater of war are enemy combatants.
The Constitution gives the Executive branch the authority to wage war and execute the war strategy. As the commander in chief the President has the constitutional authority to conduct a war. The various parts of our armed forces can and have (in previous wars such as in the First Gulf War, Vietnam War, Korean War, WWII, WWI, Spanish American War, Mexican American War, Civil War) detained enemy combatants. These enemy combatants have no standing in US courts. The armed forces follow the rules of war.
I am betting that this will be reversed in the future or will be superseded by another law.