A legitimate issue for the Supreme Court is whether or not a military tribunal for a civilian constitutes due process. The Court has not ruled on this particular set of facts (US citizen captured in the US) but the Bush Administration doesn't appear to want to take the chance the Court might see things differently.
they know they will lose the case based on some of Scalia's comments alone. we need more Thomas's but don't have them.
and it won't stop there. they will extend this same right to US citizen combatants on foreign soil, and have extended habeas rights to non citizens at Gitmo and will likely expand that also to include foreign prisoners - this is what is forcing the CIA to hop all over the world looking for prisons to hold them in.
terrorists are winning more often in the US judiciary, then on the field of battle.