Both sides waged war on civilians. Most wars are waged on civilians to one extent or another, and rebellions tend to be harder on civilians than most. And if it was Southern civilians that tended to get hit harder, well having started the war the confederacy found that they could not keep the war from coming home to them. They have nobody to blame but themselves. And if you cared to look at other rebellions througout history you would see that the South suffered less than virtually any other losing people.
I cited one example Sherman but did not mention Grants armed former Slaves in Blue uniforms.