There is no doubt many deserters were shirkers. Some came home and just hid out. Some became outlaws. The Jeff Davis administration officially recognized many partisan units and some joined up with them. If you cast a general judgement on "deserters", that is blatantly unfair.

For example, when Floyd and Pillow botched the break out at Ft. Donelson and surrendered an army of 10,000 men, it left Middle TN behind Union Lines. If I was a POW at Camp Douglas, the first thing on my mind would be to return home and join a partisan force to defend my family. The last thing on my mind would be judgement from the Confederate Army. No wait, the last thing would be judgement from anyone living 150 years in the future.