(Well perhaps except Lynata, the eccelsiarchy ends up doing kinda naughty things in that book. )
Huh? The Ecclesiarchy doing naughty things is part of the Grim Darkness™ of the setting! I'd consider it rather boring if anything in the setting was just black and white rather than shades of grey, purely as a matter of realism.
It all just comes down to how it's being pulled off and explained. In short: reasonability.
That's my point: It goes way beyond 1st SOB codex or even what Vandire was up to, that was par for the course with the ecclesiarchy. No where I draw the line is at what they were doing in RvsE:
The Eccelsiarchy teamed up with the frikkin' WORD BEARERS! Who were learning them Nunctia: magic words that Abnett pulled out of his ass. But come on! The word bearers and the church of the emperor together! Gaaah! How did that alliance happen? "Hey,you guys worship the emperor? We used to do that to. say wanna learn some magic tricks?