I believe the US government has the right and ability to detail the categorization of the extra-judicial designation of "enemy combatant." I also do believe that most people at Guantanmo are "innocent" but that the tragedies of their individual situations, which threatens to overshadow our pursuit of justice, are orthogonal to the legal issue of their designation.
It may not have been consistent with the precedent established by the Bush administration in further detailing the “enemy combatant” designation when it was decided to apply military tribunals as a method of trial to said designees as a rapid and easily implementable method by the President (ie, no need to confer with the other branches of government, Legislative or Judicial, due to the inherent extra-judicial nature of the EC designation). It would seem that a more consistent, albeit further inflammatory, path would've been to create an extra-judicial executive sponsored body of justice possibly based upon, but not exactly, existing military tribunal process.
The judicial branch is definitely concerned over matters judicial and especially concerned when their purview is sidestepped by something like the enemy combatant designation. It's also bit unsettling when legalities place areas beyond the actual, direct reach of the judicial branch. Lawyers on both sides of the issue seem to be doing the right thing by approaching the issue via one of our cornerstones of justice, habeas corpus. Whether habeas was respected by the tribunal process in place is in effect what this ruling narrowly addresses.
Their ruling today answered the question as to whether the administration's executive branch utilization of the military's tribunal system was constitutional, legal, and sufficient to adhere with their previous ruling that enemy combatants must be given a trial. They said that the President is not allowed to use the established and formal legal system of military tribunals as a means of justice. That's not what they're designed for. Enemy combatants are outside established precedent so, in essence, an existing form of adjudication cannot be used. I have to carefully read the ruling, but it may imply that even they themselves, the judicial branch, aren't the appropriate venue. This would further confirm the extra-judicial nature of the enemy combatant designation.
The question still remains as to what to do with these detainees. I'm comping up a punnet square of options for reference.