Actually, desertion, at least in the C.S. Army, was often a complicated matter. Some deserters returned to service and incurred varying degrees of punishment. Of course, some were executed and many just hid out. There were also many men who officially deserted and returned home to fight in partisan bands. This would be a special concern for men whose families and homes were behind Union lines. As long as these were partisans fighting Union troops and pro-Union homeguard thugs/outlaws, they would be just as honorable as any regular army soldier in my opinion.