You assume that the question has been fully adjudicated, and firmly established that some forces in our Civil War did commit "war crimes".
The truth of the matter is that, by their own standards and even by ours today, very few Civil War units committed "war crimes".
I listed some candidates for "war crimes" in my post #169 above, but the only one on that list actually charged & hanged, again, was Champ Ferguson: for the murder of 53 civilians.
Ferguson is the exception which proves the rule: very few Civil War "war crimes".
Of course, if you wish to redefine the term "war crime" to satisfy our most pristine moral code, then you could possibly define the entire conflict as a "war crime", and hang every one of them -- Union, Confederate, military, civilians: anybody who supported the bloody war, hang them all for your pristine definition of "war crimes", right?
Oh? You don't like that idea? Seems a bit extreme, does it?
Then why would you even consider imposing today's standards on ancestors who obviously knew in their own minds, what was a "war crime" and what wasn't?
Even at that time, the intentional killing of civilians is what I am referring to as war crimes. The soldiers of the Civil War would certainly have understood this type of killing as being a war crime, although I doubt that they would have used that exact language. They would have considered such killings “dishonorable” or something along those lines, but the point is the same.
Given that, I conceded your point that such crimes were not widespread. I would certainly not want to hold ALL the participants responsible for war crimes. There were in fact two men executed for war crimes after the war - you forgot about the commander of Andersonville Prison Camp, Henry Wirz. Nonetheless, war crimes were committed that were not punished. The winners of wars very rarely are held accountable for war crimes, so I suspect that there is very little chance that anyone in the Union army would have been prosecuted. As for Confederates, I think that Lincoln’s attitude was to allow the South to rejoin the Union on easy terms and put the whole thing behind us. Certainly, widespread prosecution of people involved in war crimes would have been contrary to that goal. Only the most egregious offenders were prosecuted, therefore. That does not mean that others were not guilty of war crimes.
Even given that, you have given one example of a person prosecuted for war crimes and I gave you another. That proves my point - war crimes were indeed committed during the Civil War. Does the fact that widespread commission of war crimes did not occur really mitigate the responsibility of those few individuals who did commit war crimes? I think not.