Maybe the Emperor doesn’t like the Imperium, but that’s probably because it’s a failed theocracy, and not because it’s a cruel, genocidal, evil, fascist regime. The Emperor was not a beacon of knowledge and enlightenment during his life, he was the end of it. I know of two human civilisations that his Space Marines snuffed out during his reign that exemplify this most of all, the Interex and one that I don’t remember the name of.
The first, the Interex, were the Anti-Imperium. There were small, only one system large, and they had knowledge at their forefront. They spread the knowledge of Chaos and the Ruinous Powers and how to deal with them amongst their citizenry, treating Psykers and other Warp or Warp-adjacent entities as scientific problems. Through this, they were nearly incorruptible. Chaos could not get a strong hold on them, because the citizens knew - “If you start manifesting otherworldly powers, and strange voices whisper to you, you’re a Psyker, you need to get help, you’re going to be okay but you can’t listen to them, they’re evil.” It was efficient and it worked. The Interex had incredibly useful technology left over from the Dark Age of Technology, as well, and could easily have rivalled the Imperium if they decided to expand. They did not, instead seeking inward perfection and scholarly pursuits. When I think Lorgar and Horus found them, they slaughtered the Interex and snuffed the light out of a far brighter civilisation.
The second, which I don’t remember the name of, was a fleet-bound society. They were peaceful and were a mix of human and alien populations. They did not want to go to war with the Imperium, and simply wanted to continue their nomadic lifestyle. Because they were full of aliens, however, the Imperium could not allow this. They purged their way through their ships, slaughtering them all until they came upon the leader of the civilisation who I recall having his last words be “We only wanted to be left alone.”
This is leaving out the time when the Salamanders, during the Great Crusade, baptised a world in fire because Eldar Exodites and humans worked together against the Dark Eldar. This is leaving out his anti-theist slaughtering of anyone who kept even harmless religions. The Emperor, I believe, would hate the Imperium. He wouldn’t hate it for the xenocides, for the oppression, for its authoritarian nature or the vile, twisted, evil things it does on a day to day basis, he would hate it because it was a theocracy. That’s it.
I don’t believe the Emperor is good. He was a fascist monster from the moment he crawled out of whatever pit on Earth he came from. He doomed the entire Galaxy to ten thousand years of mindless slaughter. I don’t believe he intended to have what’s best for humanity, either. Maybe in his weird god-mind he thought he was making things right, but I think the narrative is meant to (or should) portray him as wrong, because his methods were genocide and if he isn’t wrong, then that implies that genocide is okay, sometimes.
Sorry if I come off as hostile. This is something I’m really passionate about, because I’ve loved 40K ever since I was very young, and it pains me to see people, not you, but many people, who look at the Imperium and say “That. I want that. I want this.” even though it’s meant to be “the darkest and bloodiest regime imaginable”.