The official policy was death for desertion though a deal would try to be made if you could be found.With the implementation of the Draft Act of 1862 in 1863 more "reasons" came about. My GGGrandfather was transfered to recruiting in May of 1863 from the Army of the Cumberland which fell under the State of IL. Provost Dept.. There is an order from the Army of the Cumberland given to my GGGrandfather looking for a supposed deserter recruited from his district.He was sent to see if he went home and to be on the lookout..I mention this to show deserters were actively pursued. The man latter died ,my memory, in battle at Chickamaunga,and in fact hadn't deserted.Possibly a straggler when muster was taken. One of the "reasons" the desertion charge could be dismissed.AWOL is the term now but, French leave was used then giving the benefit of the doubt with intention to return. I don't believe there was a clemency but, the congress passed several laws after the war that would help clean up ones service record as a pension could not be achieved if desertion was on ones record.Another in my family is listed as deserted when in fact he was medically discharged because of physical issues upon muster. Signed up to another regiment ,as he wanted to serve, and was discharged for medical reasons again and never saw service.The first lists as a a medical reason for not mustering and the second as deserted when in fact he never mustered.Records then weren't like now and sometimes one hand didn't know what the other was doing.Most got their day in court so to speak.Numbers of Union deserters were in the hundreds of thousands and you don't see that many executions.I hope this helps.