Stephan makes good points below about how it would have been unthinkable to Jefferson or Washington to allow the central government to kill one out of four adult males of any seceding state, bomb its cities, burn down homes and farms, and generally wage war on the civilian population "to save the union." The Constitution unequivocally grants no such power to the central government. Lincoln acted illegally and deserved to be punished as a war criminal.
But besides that, Jefferson and Washington were Virginians. They would have fought for the Confederacy had they been alive in 1861; otherwise, they could never have been accepted again by their own families and friends. They would have done, in other words, what Robert E. Lee did. Indeed, one of Jefferson's descendants was one of the VMI cadets who was killed by the Yankee army at the Battle of New Market.