Actually, the south instituted the draft of military age men (except for those with enough slaves or money, who were exempted) before the north. It also, arbitrarily, decided that anyone who enlisted in the insurgent army had done so for the duration, even if the paper they signed said for one year, or two years, or three months. Anyone who disagreed with their feet was a deserter, and a common form of punishment for desertion in those days was death.
So yes, the military of which Lee was such an important part did indeed drag very many folks onto the battlefield.
Lee had other choices beside turning traitor and prolonging a criminal war, or "killing his relatives." He could have resigned his commission outright, and fought no one at all. Or he could have evacuated his family from the region--unlike many poor southerners who were stuck in place, Lee had the means to do so.
And while I wouldn't compare him to Pol Pot or Hitler, your comparing him to a (fictional) mother packed off to Auschwitz who had to watch as one of her children was led away to be gassed is equally, if not more, ludicrous.
If anything, I'd place Lee in the same category as Rommel or Albert Speer--gifted technocrats who served a thoroughly evil cause. But then, both Rommel and Speer eventually saw the light and tried at last to stop Hitler--for which Rommel paid with his life. Speer survived, but after the war was tried for crimes against humanity and sentenced to twenty years at Spandau Prison.
Lee was most fortunate to have escaped the usual consequences of his treason.