You're assuming the Emperor fights against an Imperium built on his visions - sure, corrupted, but not beyond saving, rather than taking over them and subjugating the alien-loving Dark Age of Tech civilization he certainly didn't have a high opinion of (but maybe that's because of how it ended up). The Imperium wasn't all that nice while the Empy still lived, y'know.
I was under the impression that he only felt it necessary to intervene when humanity was dying; hell, he probably instigated the Dark Age of Tech, what with him always subtly manipulating humanity and all that. And the Imperium, besides being really big, is (from what I know) not what Empy wants. A religion devoted to him? Nope? Genocide on a daily basis? Again nope. Repression, corruption, and generally the systems of a (necessarily) brutal bureaucracy? Nope.