Federal authorities recorded a physical description for ex-Confederates so that they could be identified by a Provost Marshal if need be. If captured while in Confederate service again and identified as having taken the oath of allegiance, a man could expect to be executed on the spot.
All we know for sure is that this man turned himself over as a deserter. There's no way we could determine whether if he really was a spy or not. In fact, Federal authorities might not be sure either. At that time people had a tendency to shoot or hang first; ask questions later.