Did Lee fight for the North?

John Avery Emison's Lincoln Uber Alles argues that the war of 1861-1865 was not the War Between the States, but the Federal Government's war on the states -- all states, north and south. Lincoln had no reservations about sending troops to any part of the country to shut down opposition to his policies and decrees. When Lee surrendered he gave up the political sovereignty of the individual states to the supremacy of the national government. The voluntary union had been replaced by a coercive union. In this sense, Robert E. Lee was fighting for the rights of states on both sides of the Mason - Dixon line. Consequently, we lost the Founder's republic and witnessed the laying of the foundation of today's leviathan state that, for propaganda purposes, still insists on celebrating Independence Day.