Treason and mercy
IMVHO, no punishment would legitimize the CSA as a State, despite Darth's comment; treason is a punishment for warring and betraying the state one is part of. And their actions fit the constitutional definition of treason perfectly.
One thought that would be, I think, perfectly legal and break the planter aristocracy completely: Offer anyone who served as an officer in the confederate army, or a rebellious state army, or any government office, a choice: trial for treason, with punishment as per the existing laws if convicted--or waive trial, plead guilty, and merely forfeit ALL property within the United States, right to own land, vote, or serve in government. (Punishment per existing laws was usually hanging--sometimes even a traitor to a STATE--when the accused wasn't even a resident of the state--John Brown comes to mind there.)
The confiscated land could be sold off to defray the cost of the war, and/or given to freed slaves...
Anyone who committed particularly heinous crimes, of course, doesn't get offered the deal.