Well you can apply that model to anything. Hitler said Jews were the ultimate evil, so it was ok to kill them.

In my view there should be a distinction between injuring/killing people and destroying their property. Killing civilians is out of bounds, but burning the cities and looting the valuables can be placed under the category of "draining the South's ability to wage war or reconsitute power after the war". It was necessary to bury the South so that it could not challenge the central government any time soon after the war. Clearly the basic ideals were the maintained after the war, so really if the South was left unscathed with its ability to regain economic power intact, what was to stop it from attempting again to rebel?