I mean, it's worth noting that usually the winners of a war do take revenge on the losers (history is written by the winners and what not). Especially in Civil Wars, where first order of business for the new government is usually to purge (counter)-revolutionaries and people from the old regime by executing them, sending them to concentration camps, etc.
The fact that the US circa 1866 didn't round up the confederate elite and sympathisers and execute them (or send them to concentration camps or jail at the very least) should be seen as an exception. Even for a democracy, normally pro-confederate sentiments would have been banned.
The American Constitution doesn't allow for banning sentiments. It was this constitution that we did in fact fight a war to preserve and thus it would be the height of historical tragedies if after the deaths of 600,000 people, we gave that up and became just like every other country.
I have no sympathy for treason or secession. I do not condone the Lost Cause and have devoted many an effort post to tearing it a new one, but there is a difference between rejecting the lost cause, decrying the horrible hypocrisy on which the Confederacy and condoning or establishing the mass extermination of the entire Southern population.
It wouldn't be "mass extermination of the Southern population". At worst you'd get "mass extermination of the Southern government", but the average Southerner wouldn't be affected for the most part. Think of Germany right after WW2 and the de-nazification policies that followed (probably an anachronism but whatever)
So you'd get whatever the equivalent of the Nuremberg trials would have been, plus people involved in the confederate cause would have lost their jobs and probably their property; plus an extra dose of censorship. The confederate flag would probably be looked at as the Nazi flag is in Germany, where just flying it would get you in trouble.
Of course I imagine this would probably enter into conflict with several provisions of the constitution, but I imagine either an activist court would get around those or constitutional amendments would be passed.