In this case, I do have to agree with the Supreme Court, which has basically said that existing US law doesn't allow the kind of tribunals that the President wants to set up put the gitmo detainees on trial. The seperation of powers argument is basically that the executive branch isn't implicitly empowered to detain, put on trial, and then punish these guys all on it's own.
Historical precedent aside (like Abraham Lincoln suspending habeus corpus) , they are interpreting current law correctly.
Now, what can be done:
1. Congress could pass a law authorizing the creation of special tribunals to try gitmo detainees. I think that might address the seperation of powers issue.
2. The can be declared POWs - in which case we can discuss the geneva convention, whether they are covered by it at all being non-uniformed combatants, and whether as POWs they can just be held until the war is declared over. If we demand the unconditional surrender of Bin Laden & AQ to end the war, it effectively becomes a life sentence.
3. They can be transferred to the civilian court system for trial - (IMHO a terrible idea).
I was definitely against the government being able to hold Jose Padilla (an american citizen) at gitmo without charging him. The courts past ruling on him addressed that concern, and I think today's ruling shows that the court is watching and seeking to strike a balance between individual rights and the government's power during time of war.
EagleDNY
$.02