The partnership of Lee and Jackson kept the Confederacy alive, even though its fortunes were fading from the very beginning in the West. Lee represented the Episcopalian elite of the lowlands, while Jackson represented the more Presbyterian culture of the highlands. Both were great men, and neither fought primarily to preserve slavery. They fought to defend their state against imperialist Federal forces.
Loyalty and patriotism were understood in those days in this priorty: 1)Family, 2)State, 3)Nation.
When Lee’s state, Virginia, reluctanty, but lawfully, voted to secede from the Union, he felt he had no choice, though he was against secession, but go with them. Wars of one part of the government (the states) vs. another, (the federals) do that....and gentlemen of good conscience, loyal Christians too, can disagree on which way to go.
Similarly in the American War of Independence,where the colonial legislatures chose to rebel against the English Crown, although we as patriotic Americans are loath to admit it, there were good men on both sides—Patriot, and Tory.