The main criticism you can level against Lee is that he prolonged the war by his superior generalship. If he had refused to join the South the Confederacy would have collapsed much sooner, sparing a lot of death and devastation. But, who knows? An early Northern victory might have been worse, setting up a second civil war. The south was totally beaten by Appomattox. If they had collapsed sooner, the “stab in the back” idea might have remained, much as WWI lead to WWII.
But even so, of course Lee wasn’t the plaster saint that some people believe in, no one is. That doesn’t mean he was a monster or even a jerk. Judged by modern standards he falls short of course, but to a lesser extent than almost all of his contemporaries.
Now, the devastation of the south. Of course the war devastated the south. But it was the war that devastated the south, not occupation and reconstruction.
Now, criticism of Grant. Well, Grant realized that he couldn’t match Lee head on. So, he decided to play to the North’s strength, superiority in manpower and manufacturing. Sure, a brilliant general could have outflanked Lee and won the war in one glorious stroke. But there were lots of northern generals who tried this and didn’t succeed. Grant realized that this wasn’t going to happen and decided to win the war the only way he could, through attrition.
Now, why wasn’t the Southern leadership lined up and shot after the war? Well, what would that accomplish? It would have re-ignited the war…if not right away then soon. Whether they deserved to be treated as traitors or not it would have been severely counter-productive. It would have destroyed the idea of re-union, the south would have to have been occupied like a foreign country rather than re-admitted into the union.
Oh, and slavery WAS the main cause of the war. Yes, it was state’s rights…the rights to own slaves. No slavery, no war. Jefferson and the founders realized that slavery was a blot on the republic, but they consciously decided to compromise on the issue to allow formation of the Union. They expected that slavery would wither away in a generation or two, and the promise of the founding would eventually be applied to all. As MEBuckner has ably pointed out they knew slavery was wrong but felt they could not tackle the issue in their time. Well, slavery didn’t wither away and it turns out that they miscalculated and their compromise allowed the entrenchment of a particularly brutal form of slavery.