Disqualifying the moral opposition
If we have a bishop seeking to impose theocratic rule, he must be a pedophile. At the very least, he must be shown to be a gross hypocrite in some fashion or other. It is only our hero who is consistent in his beliefs. The same thing goes if our antagonist is a capitalist, communist, believer in “might makes right”, or whatever moral idea we might choose to vilify. It is not enough that our antagonist be wrong, he must also be a hypocrite.
If our bishop is an incorruptible man who practices what he preaches and is surrounded by loyal follower who love and respect him for what he is then it makes it that much more complicated for our hero to fight against him. The moral dilemmas are harder if the man is wrong but not a hypocrite. It is much harder to butcher off honest believers then it is to butcher off cynical hypocritical opportunists.
We hate such complications. So we make things simpler on ourselves. We conjure up images of Hitler, Stalin, and the Spanish inquisition to justify our moral simplicity. We willfully forget that the Finns fought on the side of Hitler and Churchill fought on the side of Stalin. Or we remember these things and cynically decided that there is no moral order and it doesn’t really make any difference what you do as long as you win.
But a painting that is all black is the only thing that has a simpler color scheme then painting that is done in black and white. Saying that everyone is equally amoral is the only thing that is simpler than saying that there are good guys and bad guys. Complexity comes when the moral ideas that you feel are wrong are held by people who are no more hypocritical then you are.
That is not to say that the righteous hero has no place in myth. Myth is for distilling abstract ideas into concrete realities. But to achieve moral complexity the antagonist of our hero must be equally pure. Our nature loving “good” Witch must be pursued by a Paladin who is as brave and pure as he is convinced that Witches must be wiped off the face of the earth. If we want our story to be morally complex the resolution to their conflict must be as tragic as it is heroic. We should not feel triumphant at the death of the Paladin even if that is how the story has to end.