Deserters where punished, but it depends on why they deserted. Some where shot, branded, or sentenced to the iron ball and chain hard labor . It also depends on the number of times he deserted and whether he volunteerly returned to the unit. They was usually a hearing in front of a board and punishment given. I have a letter from Stonewalls old regiment that say's a man was caught for deserting and tied to a stake and shot.Its interesting that Jefferson Davis pardoned must men that where to be shot. But if their's no punishment than their is no displine so your army may dissolve. Keep in mind that some of the soldiers that where listed as deserters where not. GS