The Milgram experiment shows us not that people are inherently evil, malicious or spiteful but that in the right social context people will follow an authority figure's instructions even if it overrides their normal moral response.
What exactly is the difference? If you substitute an authority's conscience for your own, you are inherently evil. It is this reaction that is responsible for the great majority of evil in the world.
The sickest psychopath in the world is capable of killing a few dozen people on his own. But a psychopathic leader is capable of killing millions. All that extra blood isn't really on the hands of the leader, it's on the hands of those who chose to follow that leader. Those who thought obedience was the best thing. That's where true evil comes from.
I don't see how this is complicated at all. Authoritarianism is evil, and most people are authoritarians. Ergo, most people are evil.
One of the interpretations of this behaviour by Milgram himself: "the essence of obedience consists in the fact that a person comes to view themselves as the instrument for carrying out another person's wishes, and they therefore no longer see themselves as responsible for their actions. Once this critical shift of viewpoint has occurred in the person, all of the essential features of obedience follow".
And in this case I agree with Milgram, if it is the case that people shed moral responsibility and adopt the aspect of a tool, instrument or cog in the machine when dealing with an authority figure demanding they do something they find personally amoral then it seems to me to be a defence mechanism to protect and preserve their own moral viewpoint as the other alternatives are:
1. Defy the authority figure, possibly be fired, suffer a court martial or be shot depending on the situation
2. Change your moral beliefs to match those of the authority figure
Since, I would argue, most people have a preference for not being shot and an affinity towards good moral thought and behaviour they can't reasonably choose 1 or 2 and so are left with:
3. Shed moral responsibility for the action and leave that responsibility to the decision maker and authority figure.
It shouldn't be inferred from the Milgram or Stanford experiments that all humans are evil given the right circumstances, but rather, that given the right circumstances good people can do evil or amoral things.