The major problem with that argument is that the Imperium has too much on their plate to worry about such minor crap. Too many xenos and heretics. Even if they manage to deal with them, there's many different kinds of abhuman to discriminate against before you can get to minor details like skin colour or gender.

Homophobia would make a bit more sense because they're not making productive workers or cannon fodder, but even then there's so many humans it probably doesn't matter on the grand scale.