The war between the states was not one to free the slaves until AFTER Antietem, and then only by decree from Lincoln. it was at first a war to preserve the Union, to force the seceding states back into the nation.
The states and a lot of the founding fathers had little faith in a central government, and knew that would be a detriment to their way of life.
Lee believed that and Virginia was his 'country' if you will. The Emancipation Proclimation condemned the South to fight for a cause that was not an issue for a lot of them.
Lee was respected by the North, and loved by the men of the South. He could inspire them to great things, but could not make up for poor nutrition, poor clothing, poor armaments. The Napolianic theory of the 'great battle' was over due to advances in riflery and artillery. But niether side had any real 'thinkers' who realized this evolution until Grant.
I'm a Southerner, but that's just plain factually incorrect. The seccession documents of EVERY single southern state name Federal intervention on slavery as the primary cause of their secession.