Hopefully I'm preaching to the choir and the main response from everybody is that this is obvious and didn't need to be said.
I read a few comments from some gross cishets about how angry they are about the female Custode. They prop up the Imperium of Man as though they are some paragon of morality and not the picture of everything wrong with imperialism. Naturally this perfectly moral force would have only men in its ranks, clearly! They don't seem to realize that if women are left out we have a sexist/mysogynist system which is not worth praising, and if they include women then it's the imperialist machine trying to keep up appearances. Frankly, I've always figured the Imperium didn't care about gender or race because everyone is suitable to die in combat and be ground into food for the starving populace.
tl;dr Men are upset that women exist and missed the whole satire
Yeah, but the humans and other races they seek to integrate into their society aren't. They'd either have to do some necron-tier shit and destroy the souls of their citizens or they'd be at risk of humans creating a new chaos god.
Another option is they may decide that warp-sensitive races are too much of a risk to the galaxy and adopt a genocidal attitude for the greater good. That would be thematically appropriate for Warhammer 40k. A bad encounter with the effects of the warp leading to them abandoning their previous principles. Kinda like how the Horus Heresy affected the Imperium of Man.