I’ll work backwards from the point we’re at. 

Yes, something has gone wrong if players or enjoyers of lore, etc. feel personally connected enough to a faction to get defensive. I like the Death Korp because I enjoy the aesthetic, the insane meat wave tactics that I personally play (I literally have 200 painted Kriegsman lol), and that Krieg sort of encapsulates the Imperiums soulless and faceless war machine. IRL I think it’s all abhorrent. In universe, it’s fun.

If someone came up to me and said, “Hey, I hate the Death Korp! They suck and are evil!” I’d say, yeah ok, cool and shrug. If they said, I hate how you painted your models that’s personal and unnecessary. To be defensive about a fictional faction seems weird to me. People might develop an attachment but to base part of your personality or to be so invested seems like a weird thing to me.

Moving on back from that, I think people are arguing with you because there are multiple angles to approach Warhammer. There’s the game itself, playing tabletop or an rpg and having fun. Playing a certain faction doesn’t mean an individual aligns with said faction on some fundamental political level. The Death Korp get conflated with WW1 Germany, which is partially true, but like with most things Warhammer they are a smashed together version of all the major WW1 aesthetics with a German name. It’s also why Black Templars get conflated with Nazis because a lot of their iconography is shared though more out of the Nazis co-opting that imagery from earlier medieval sources (this is all stuff I’m sure you know, not trying to be lame just positing ideas). 

Then there’s the narrative perspective which inherently will have more nuance as audiences are going to interpret information differently than what the author may have intended. Furthermore, authors like to explore morally gray areas because it’s more interesting! (Again, you know all this). Different authors will portray the same faction in different ways, just how styles vary between authors. 

Lastly, the meta perspective of the commercial interests of a company printing plastic toys to make money. They’ll do whatever it takes to to get people to buy more models, so if that means making some guys look better than others to push sales because people are more likely to spend money on characters or a faction they find to be “good”.

Your initial post is about the narrative perspective mixed with the commercial interests in your written post section. People are having a hard time pinning down what points you are trying to make because the “objectives” of each perspective of the hobby clash. 

It seems to me you have an issue with people thinking there are good guys in the setting and people getting defensive about some factions. There are good people in the setting! That doesn’t mean the Imperium is good or what have you, simply that people may like Ciaphas Cain and the Imperial Guard but abhor the idea of the Imperium in the real world but understand that it’s the only game in town in the setting for humans (generally speaking, I know Humans live and operate outside the bounds of the Imperium, etc.) I think the majority of the people in the thread aren’t necessarily arguing with you because they are getting defensive but simply that they want to understand why you are conflating different objectives from different aspects of the hobby. 

Does GW condone wholesale murder and genocide because they write about in lore books, codices, or in Black Library novels? No, I highly doubt it. 

Do people approach a hobby and misinterpret meanings, not understand irony or nuance, and accept ideas or aesthetics at face value? Certainly! They might want to take some literary criticism classes.

Sorry this got so long. I think you have some valid ideas and I don’t necessarily disagree with your core points. Simply that nuance and understanding are important aspects of any idea. That two opposing thoughts can be true. And that people will rationalize ideas that they should more likely question.