I think the Supreme Court was wrong to rule as it did when it comes to the enemy combatants that were captured overseas. However, I also see no reason why these guys couldn’t have been tried by some sort of military panel shortly after they were picked up.
The factual history says at least Boumedien (I haven't checked the others) was picked up in Bosnia, after the Bosnian courts found insufficient evidence to hold them. The judge looked at the US government's evidence, a classified document from an unnamed source.
That secret document, which the judge said he could not evaluate for credibility or corroboration because the government had not given him information enabling him to do so, did not convince him that the five had a plan to fight against the U.S. or its allies, or even knew of such a plan.
SCOTUSblog: Judge orders five detainees freed