I am also not a lawyer, but if the government really just wanted their conviction of this one guy, the obvious path seems to be to abandon the court order to decrypt the drive, and just move forward with trial based on the forensic evidence from the system root. Slapping him with contempt on this, and continuing to sweat him out in jail while he files higher and higher appeals, is the government's decision.

Getting the Supremes' opinion on this is kind of a superposition of states: if they decide in favor of right-to-encrypt, that's great, as suddenly the government will (presumably) stop using these kinds of court orders; but if they find against, then it's worse than the current uncertain situation, as orders to decrypt will then become an accepted tool. If the Supremes would find in favor of compelled decryption, then I'd prefer it never go to them, and remain in the current legal limbo.