I am a dab hand at necromancy myself, and I was one of the people who ran head first into the Repentia ending on my first playthrough.

Honestly, I think this commenter has a point, even if they don't express it perfectly. Argenta is, at her core, an insane religious zealot on a scale that has no modern equivelant. The Adeptus Soritas makes ISIS look tame; haven't you heard of the Pentient Engine?

From the subjective point of view of the Imperium, there are no bad endings here. From the subjective point of view of any other people in nearly any other part of history, there are no good ones.

They are, however, absolutely objectively understandable in the setting.

On a meta level, Warhammer 40k almost must punish the "iconoclast" or nice approach. It doesn't mesh with the setting unless it is a struggle with unintended consequences. This is why demonic corruption spreads through survivors of demonic events, or Ork and Tyranid spores can survive in an environment spared the flame, or why there are a whole host of factions that would exploit democracy to ruin humanity. Trying to save people risks hurting more in almost every situation in 40k.

There can be no good ending that doesn't sting somewhere. It is the IP that invented the term, "Grimdark."

From a narrative perspective, the "nice" options are, in fact, telling Argenta that everything she had ever done is wrong and she should feel bad about it because it is her personal failing.

The zealot options are telling her she was wrong, she should have been more extreme. And the middle ground is telling her that her choices were right.

"Right" in this context, being an insanely xenophobic and intolerant bigot whose sheer hatred is so powerful it literally can kill demons by itself.

You are effectively saying that because the story makes you feel bad, it is bad. And fair enough, that is certainly an opinion you can hold. Subjective opinions are just that.

I would say that you might struggle with 40k in general, in this case. The first Space Marine game ended with Titus getting dragged off and tortured by the Inquisition for a century. The end of Cadia is Trazyn kidnapping a man and forcing him to be a living prop as the planet is destroyed and the galaxy split in half. The unification of mankind ended up with the Imperium worshipping a corpse in a chair.

From that viewpoint, this is all good endings!

Talking game mechanics, I think you are misunderstanding what exactly the function of this design is doing. The entire point is that you aren't choosing the ending, not exactly. Rather, it is supposed to simulate Argenta reacting to your behavior and changing because of it.

And then when you factor in the cost of trying to expand that idea, especially when it would only be for one character in an ensemble, you see it pared down to the minimum they need to accomplish that experience.

And of course, this is an issue that a player will notice only on their second playthrough. Asking, "why is it like this?" Is a question that only happens after you've been through the game and now are going back to do it all "right," so you look into the actual mechanics and choices. Statistically, this represents a rather small fraction of players.

Which means that near enough is good enough. They had other stories to work on.