My senior thesis research has been on the Conscription Act in North Carolina.

The issues surrounding conscription there were often met with harsh negative sentiment or desertion, even to the level of full scale mutinies. Often when people speak of desertion they see it as a fear of battle. In the North Carolina and the south that was not necessarily the case. Most men wanted to fight and defend their way of life.The biggest issue with desertion was simply that men wanted to take care of their families. When word got around that their families were starving and not being properly cared for many simply just left. That, or if they were a fresh conscript and nobody was paying attention to them they would simply just leave camp and go home. In North Carolina desertion was also a form of protest against the Confederate Government, who so desperately needed soldiers, because many Carolinians felt that the Conscription Act violated their State's right. It was enacting the same sort of overpowering Federal laws that the United States had before secession, so it was a problem of "well why did we secede just to have our new government do the same thing".

Hope that helps some =D

Which Civil War?