In the book “Lee: The Last Years” by Charles Bracelen Flood he notes that none of the southern leadership, including Lee, was ever tried for treason. He says that Salmon P. Chase, who was then Chief Justice, told Federal Prosecutors to not try it because they might not get a conviction and that would set a bad precedent.
I have actually ran across quoted bits of this discussion, and if memory serves me right, I believe what Justice Chase said was "You will lose everything in the courtroom that you gained on the battlefield."