In the DH/RT campaigns I've played so far, my teams committed lots of atrocities in Emprah's name. Torture, blackmail, slavery (including sexual slavery), judicious use of psychic reprogramming, sabotaging imperial institutions, wantonly causing civilian casualties, you name it. Some of this stuff was openly endorsed by the Inquisition, some was private initiative, but we always managed to get away with it because we could always prove it was for the good of the Imperium, or just nobody cared. In the current DH campaign I'm in, I'm playing an Administratum adept who flirts with dark powers and abuses his administrative privileges to destroy his opponents in the race for the planetary governor's seat. And as far as player characters go, I'm still among the most concerned about the fate of Imperium.
I honestly don't think having more non-consensual sex or killing some children or whatever may come up in a Black Crusade game can really make the experience somehow more palpably evil. We'll be doing the same stuff, except we'll be working for someone else, and might get cooler powers out of it.