The real problem with the War of Nurtheren Agression was the reconstruction time. both sides continued the partisan and bitter politics instead of doing what the warriors did and bury the hatchet.
Clearly the Federal government used the War, righteous or not, to wield tremendous power over the states, and the unfortunate consequences that have followed still plauge our country today.
I think the drastic measures used by Lincoln may have been necessary, but should have been given solid, unimpeachable sunset provisions. The Income Tax, very questionable property rights laws, and near Marshal Law powers for the U.S. Military were allowed that would have been thrown off by revolution by most of our founding fathers were the hopefully unintended consequences of the war.
There should have been apologies all around, there was plenty of blame to spread around. If you look at the fighting men on both sides, fighting their own contrymen, if not family and friends, I don't know if there is a way to balance the positive and negative results of the war. It really was a Lose-Lose in many ways.