I’m with @mathbrush on this one: once a game has been released, and had effects on the world, removing it from an index doesn’t erase those effects. They’re part of history, and trying to erase the traces they’ve made never really removes those traces. I’m talking here not just about the “you can never really delete things from the Internet” discussion that’s used to finger-wag at children getting their first social media account, but the deeper issue that creative and expressive works change the people who encounter them as well as affecting the people who produced them. That’s the deal with producing a creative work: it needs a viewer/reader/player/interactor/encounterer to have any meaning in the first place, and putting it out into the world is necessarily accepting that bargain (and, usually, intending to enjoy at least the positive aspects of it).
To take an example from a different genre (and intentionally not commenting on the game in question, which I cannot identify and probably have never played): Arthur Conan Doyle said some pretty racist and misogynistic things in some of his fiction. That doesn’t mean “he wasn’t a good writer” in some other ways, but it does mean that he said racist and misogynistic things in print, and that’s part of his legacy. That he didn’t know any better than many people in his society at the same time isn’t the same thing as not having those things. But more to the point, the things that he wrote are a valuable way of looking not just at the question of what he, personally, believed, but also of getting at what Victorian and early 20th-century society thought about race and gender. Covering up those things doesn’t just bowdlerize Sherlock Holmes to rehabilitate Doyle, but also presents a cheery but false picture of what British society as a whole thought about those subjects at the time.
Or, to take an example from a much different genre, again not commenting on the game in question: the last president of the US had a habit of saying particularly vile things on social media, then deleting his posts after a few days. But those things still went out into the world and influenced his followers before they went (in Orwell’s phrase) down the memory-hole. But even after they were deleted, it matters that he said them: they worked to build up the kind of society he wanted to build up before they disappeared. People who archived them were, I think, doing valuable work, despite the fact that the person writing them had reconsidered what he’d said, and whatever basis he might have had in an individual case for reconsidering that decision, it still matters that he said them. it had tangible effects on the world.
To pick an example closer to home: the original Stiffy Makane is a terrible piece of IF on a lot of levels, from its many forms of misogyny to the epic over-promise in the title and its terrible design. But it’s had an impact on (and outside of) the community, in part by inspiring spoof games that are much better than it is, and in part by serving as an example of many things not to do when writing interactive fiction (and writing in general). But it’s also a data point for anyone looking back at any intersection of the end of the twentieth century, interactive fiction, pornographic writing, misogyny, narrative … It should continue to be indexed, because it doesn’t just reflect on the author: it reflects on our society, on the community, on the possibilities for interactive narrative. Pretending it never existed would be deeply dishonest in many ways. Now that it’s out there, it’s part of the world, and that’s a decision that the author made, underage as he was at the time, when he released it. Other people have built upon it, and it’s had an influence on many other people’s lives. It doesn’t just belong to him any more; it belongs to everyone who’s built on it, played it, or had their lives affected by it, directly or indirectly. De-indexing it because it’s embarrassing to the author is not just dishonest, but a violation of other people’s experiences.
Though I am not trans and have never transitioned, the “should we keep using the deadname” question seems to me like a poor analogy here. Using a person’s post-transition name, even for works written before they adopted that name, seems more like a question of updating the metadata for a published work than pretending that that work never happened. I know scholars who prefer to be referred to by their post-transition names, even on work published before they transitioned. I don’t know scholars who ask that no one ever refer to their pre-transition work on the basis of their transition.
I’m not saying that nothing should ever be removed, nor am I saying that the author’s view doesn’t matter. But I am saying that once something’s been published, it doesn’t just belong to the author any more. If communication is happening at all, it affects other people, and a massive index should include things even if the author regrets them.