Do you have any historical knowledge of how the losers in other great civil wars were treated?
In the English Civil Wars the leaders (and many of the followers) were proscribed, their property confiscated and they were often executed.
In the Spanish Civil War somewhere between 100,000 and 500,000 of the losing side were executed after the war was over.
In the Taiping Rebellion, which took place about the same time as our War, 20M to 30M people died, many of them civilians massacred by the Manchu after the end of the fighting.
After the WBTS, the number executed in revenge by the winners was somewhat smaller. Exactly one, in fact.
It would be interesting to know how many South Vietnamese were killed by the Communists after their victory in 1975--again, a civil war from one perspective (the North's)--but there was an unspoken agreement after the fall of South Vietnam not to learn how many were killed by the Communists. Tito killed many of his opponents after winning what was both a civil war and a war against foreign occupation.
Charles II had a few of those most responsible for his father's beheading executed. Later, when Bacon's Rebellion was put down in Virginia, he was upset at the governor of Virginia for killing more people in punishment for that than he had killed for killing his father.