As a matter of fact there were several dispatches which issued instruction to the effect that officers who resigned their commission could be drafted if they fell under the provisions of the Conscription Acts.

This was especially the case during the reorganization in the Confederate Army after April 1862, where officers who were either not re-elected to their rank, or were found unfit by a review board for their rank, were subject to being drafted as privates under the Conscription Act.

So this idea that a person could sit the war out being neutral, after the Concription Acts in both the North and South were passed, was pretty much non existant, especially in the South.

Lee's age would have been an exemptions so he could have sat out the war had he chose to.