[@Letter Bee]
Personally, I find that someone who finds everything that in-canon implies that a religion could be used for evil (not even that the people participating in it are evil) is offensive is in and of itself ludicrous. There are entire churches devoted to informing the world that, outside of any fictional sense, anyone who does not worship Jesus is inherently evil, and therefore deserves to burn in hell. The Bible itself is explicitly offensive to anyone not part of the religion. If we're talking about a piece of fiction that demonizes a group of people I would argue that your religious texts are more offensive than anything 40K can offer. The Emperor was a scientist who believed Religion to be a tool for superstition and chaos, and was correct, so he removed it. In-universe his actions were logical and just, and you cannot call him evil because you interpret his actions as representing an out-of-universe bias or are offended by the implications the in-universe act has in relation to your real-world beliefs.

This has been a long-running discussion which I have no intention of revisiting, but you should learn to seperate the actions of a character in a work of fiction from any real-world interpretation of the meaning behind those actions. You should also learn that some universes simply have religions as being used as a tool for evil, live with it. There are plenty of fictional universes where Christianity can be weaponized to kill demons or whatever. But demanding that every work of fiction in the universe depicts your favourite little group as being exclusively nice is simply not realistic. By those standards you wouldn't be allowed to print any religious texts whatsoever, nor vampire stories where holy water is used to fight vampires, or anything in a similar vein.

If you wish to have a serious discussion about theology and it's application in modern pop culture I would be happy to oblige. Hit me up on skype or send me a PM, and we can both debate our points. But this is not the time or the place, and therefore I declare this argument ended on this page, for the moment.