While what they did may be considered war crimes today, there was no Geneva Conventions until 1864. The treaties affecting treatment of civilians during wartime were not adopted until 1949. It wasn't against international law until then. The USA had been placed under martial law, so the law was basically what Lincoln said it was.
So technically speaking, there were no war crimes during the civil war.
The discussion of the loss of states rights, loss of individual rights and the federal power grab is more interesting. These issues are directly related to the topic you posted.
That's ridiculous. War crimes are war crimes, and the law was not "basically what Lincoln said it was." Lincoln had no jurisdiction over the Confederate States. Destroying southern towns and murdering, raping, and pillaging southern slaves and civilians are war crimes.
Technically means just that. There were no laws against attacking civilians, Lincoln was bound only by 'moral' law.
From Lincoln's point of view, the Confederate states were still part of the Union, that's kinda why they fought a war.
During times of martial law, the executive in chief makes the rules. The law was whatever Lincoln said it was once he declared martial law. Martial law was one of the political/legal means he used to make the war "legal".
If Obama declared martial law today, whatever he decided was best would be law, and enforced by the military. Check the constitution.