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That was what the South was fighting about - Lee really did represent it. The dedication to family and family name, both establishing it and cleaning it up! - the honor code, the women who were so dedicated to preserving their plantations and their society. Mary was as much a driving force behind Lee's decision as could be. (They should have recruited the women - there'd be a Confederacy now!)
Diane, I think you have come very close to hitting the nail on the head. I think it would be worthy of a thread unto itself. If you think about it, the Confederacy from it's infancy, during the war, and for a long time after, was born, nurtured and raised by the women of the South. In the beginning, the men were urged off to war and pretty much told.... don't come home until you whoop those Yankee's *** back to Boston. After the war, the wives were probably the biggest reason for the establishment of the KKK, when they once again urged off the men to go fight for their women's honor and protection through reconstruction, and then, in 1894, the establishment of the United Daughters. In my family, from Middle Tennessee, all my g grandmothers and aunts were members of both the DAR and the UDC, with history back to the 1600's in Virginia and Maryland. The majority of the family had been slave holders, so your mentioning the women's dedication to the plantations and their society really hit home.
In that light, Robert E. Lee, married to Miss Custis, really had no other choice than the one he made. The honor code wouldn't have allowed him to. I believe that Lee understood the ramifications of his decision very well. I don't think he had any illusions of the reality of it all. Then, it was in for an inch, in for a mile. Stiff upper lip and tally ho.
I can agree that you have to balance the memory of the man with both his accomplishments and his faults. Yes, he fought to perpetuate the already dying institution of slavery and we should remember that. As has been mentioned, in the end, he was just a man. He wasn't really made of marble, but he was more marble like than most, in his time.