Rebellion is no more legal than bank robbery is. Criminal charges may not have been applicable but there is no doubt what the South did and that they paid a penalty for their actions.
Actually, there were a lot of questions in the minds of serious people both before and after Lincoln's War about the South's course of action.
Look no further than the archetype Republican D. D. Eisenhower. It was he who wrote to a South-hater in 1960: “I would say, first, that we need to understand that at the time of the War between the States the issue of secession had remained unresolved for more than 70 years. Men of probity, character, public standing and unquestioned loyalty, both North and South, had disagreed over this issue as a matter of principle from the day our Constitution was adopted.”
The supposed criminal offense of secession is not quite the picture you paint.
While there may have been room for men of goodwill to disagree at one time about intended limits on the the size and scope of the federal government, it is now too clear to deny the South was right in opposing corrupt, incompetent federal overreach and deadly tyranny.