I know that the Imperium of Man has a very low view on mutants in general, expecially after the Horus Heresy. However I was wondering what the God-Emperor thought of the mutants before he was confined to the Golden Throne. I can understand if he hated those who were affiliated with Chaos, but what about Mutants who largely were still human-looking and were still loyal to the Imperium? Did the Emperor care about them?
What I know is that he let mutants join Imperial Army and maybe gave them equal rights when effects of the warp wasn´t involved. There is no proof he hated them. UPDATED: Some sources say if Imperial Webway network would have been completed, Emperor would have the Navigators put to death like the thunder warriors were after Unification wars.