The whole of the Imperium is hypocritical. They fight to preserve humanity, yet they are the biggest destroyers of humanity. Purges, repression, brainwashing/indoctrination, slavery just to name a few of the practices directed towards their own. Sound familiar?
I have to say that the Imperium are the biggest bad-guys of them all. Chaos wants the freedom to do as they choose, Eldar want to survive, Orks want to fight, Tyranids eat, Necrons harvest and so on. Only the Imperium mass-murders it's own people so freely and unthinkingly. They praise ignorance and damn the enlightened/intellectual souls. Humanity's greatest strengths are repressed in favor of blind obedience and servitude. Individuality is a crime punishable by the death of worlds. Ruthless dictators control the populace of planets with an iron fist in the name of a dead magician who sits on a golden throne uncaring for the billions of lives ended in suffering every day. The same corpse-god feeds on the souls of thousands of his own subjects every day to slow the coming of the inevitable oblivion that he is surely and steadily slipping into.
I may play Space Marines, but that's only because I like to play the bad guy.