Interestingly, this question has come up a lot in recent weeks! I posted a reply not that long ago, here: https://www.reddit.com/r/AskHistorians/comments/6tios5/why_were_there_no_nuremburgtype_trials_for/

Feel free to comment with any follow-ups!

TD;LR - Lincoln was clear in the weeks leading up to the end of the war that he didn't want to prosecute the Confederacy or pursue a hard peace.