Guilliman is as Imperial as Imperial can get, yes, but judging from his comments and behavior in the various 30k novels, he viewed the Imperium's conquest and brutality as a transitory period. The birthing pains before something greater, if you'll pardon the metaphor. He envisioned a galaxy where each planet was ruled by a Space Marine, who were designed by the Emperor to excel in all things, and so the future was bright. After the Heresy, he put forth the Codex Astartes specifically to prevent anything like it from happening again. The Imperium wasn't secure, not truly, but it had survived, and they were intact enough to rebuild. Even without the Emperor's direct guidance, surely, with the remainder of his brothers they could build something worth the struggle (keep in mind he disappeared centuries before the first Black Crusade; I'm pretty sure he even disappeared before the Inquisition or Ecclesiarchy came to real prominence though I know the former existed in some capacity)
Then one day he wakes up to find that the Imperium has fallen so far off the rails that it's become everything he, his brothers and his father fought to prevent. Why even defeat Horus at all if the same result was going to come about anyway?