I have no doubt that many military leaders would defy commands to kill non-aggressors that they have a sense of kinship with. Unlike the civil war, we don't have the moral high ground provided by slaver to drive men to kill their brothers.

I suspect that the federal government would try to negotiate a secession that gave them some power over the newly formed nation, in order to "give the people what they want" while maintaining the status quo as much as possible.