Anubissama, I hear you, I really do. But there’s a few things that I want to mention.
1. Fighting the outsiders and wanting them out of our reality isn’t really a morally upright or morally evil thing; it’s just simply survival. Per Word of Jim (and I don’t have the exact reference) this is a battle in which both God and Satan would be on the same side. Pretty much, if you live in the Dresdenverse, and you know about the Outsiders, and you’re not so delusional as to think that you can control *them*, you’re against them.
2. Jim’s stated in one of his talks on writing that the key to making a really good villain is to remember that in his mind, he’s the hero of his own story. This is something that people often forget: most people, regardless of how upright or twisted they are, generally live their lives doing what they feel is right in their own eyes. Few people wake up and just think, “You know what? I’m going to be a complete monster today.”
To the Fallen, I’m pretty sure it did seem like some sort of act of liberation against a brutal tyrant. And that the Knights and those who serve TWG are nothing more than a vicious military police focused on bringing them to knee in submission. That does not mean that this position is correct, but it means that they've justified their actions and motives. An emotional abuser may lie and manipulate and stalk not because they hate the person, but because they love the person and can't live without them. A freedom fighter may strike a blow against the heart of the Empire that's choking out their way of life, 100% certain that they're doing the right thing, and we remember them as terrorists who hijacked a plane full of innocent civilians to kill thousands more. Feeling that you're in the right does not make you objectively good. Which brings me to my third and final point
3. The end rarely justifies the means. One of the prevailing themes of the Dresden Files is that there’s always a way out; always a choice to be made in which one can still save the day without turning into a monster. If you’ve gone down the left-hand path to the point in which you’re slaughtering innocents without a second thought, it’s long past time to consider that possibly you’re not the hero that you thought that you were. That’s so central to Harry’s struggle against his internal darkness, and therefore central to the Dresden Files itself, that I honestly feel that if you disagree with that you’re probably reading the wrong book.
Good intentions are nice and all, but it’s what a person does that really indicates who they are. You can fairly judge the type of men that the Knights are from the work that they do. And, I believe, you can fairly judge Mab and Nicodemus based off of that as well.
Long story short: If Nicodemus’ solution to stopping the Outsiders from destroying the world is to turn it into a nightmarish hellscape full of death, ruin, and destruction, then I’m not sure that he really saved the world from destruction at all.