Nothing he does will actually repair what he has done in the past. It will not bring back the lives or the civilization he has destroyed. It will just destroy several more civilizations. He scoffs at 'human justice' when they are about to punish murder with another murder. Well, his idea of justice seems to be human justice to the n-th degree.
Also: Did he replace some perfect world with some sort of complete hell? If the old world was so great, why did he have to create the Veil? There was magic, immortality, and great 'technological' achievements (if we consider magic to be part of the technology of Thedas). There was also slavery, vendettas, and wars that tore apart the Empire.
Currently Thedas has circles, wars, stupid mages who corrupt spirits. There's also nugs, people who sing as they unite to fight for their home, people like Mother Giselle who help the refugees, good friends like Varric and Swan Pricesses of Awesome like Josephine.
What will the world that Fen'Harel creates have? We don't even know, but my guess: just as much good and bad as any other world.
Imagine you wake up one day and realize that your modern society had been replaced by something akin from the Dark Ages. Lots of knowledge, technology, and civilization gone, and you might be burned for saying the Earth is round. But people are people, they have love, children, friends, jsut like we have them today.
Is your solution going to be: Let's kill all of these people, so that my few surviving fellows can occupy the land and build anew?
Or would you go for: This is sad. I will do my best to make as many positive changes as possible. It will be a slow and painful process, and the end result will require more than my own effort, so this world might not end up exactly as I want it to. But I will do my part to improve it.
Think of it: He has so much power now. He has rallied agents behind him. If he used all this to change Thedas instead of annihilating it, wouldn't he be able to accomplish a lot?