That's just ashine. An author can't explore dark themes without personally endorsing the acts that make it dark?
It's not the exploration of the theme, it's the way in which it is explored. This exact same game WITHOUT the armchair philosophy would be perfectly admissible, and probably superior. WITH the armchair philosophy, it becomes a discussion on the moral ambiguity of things that are not morally ambiguous. The difference is subtle: Sensei's voice changes sometimes, such that his lines appear to come from an omniscient narrator rather than from the protagonist's monologues. In particular, this happens during Happy Scenes. At first I put it down to Selebus attempting to convey trauma or just playing with the fourth wall, in which case the exploration of the depravity of a traumatized man or of religious themes would be legitimate and interesting topics. However, the voice (the way in which the speech is structured) is too inconsistent to represent trauma or a divine presence, so I can only attribute it to an omniscient narrator: Selebus himself. The only way this could possibly be justified otherwise would be by assuming some multiple personality circumstance for Sensei, either as an actual psychological disorder or as some kind of supernatural possession. I dismiss the latter as unlikely due to several hints thrown in throughout the game, and the former as there is no indication that this would be the case.
Again, I do find the writing to be excellent and the stories and traumas of individual characters to be very interesting, so much so that I'm still playing it. It's the discussions on the morality of certain activities, specifically grooming, religiousness and the treatment of depression and nihilism, that is lacking in substance. He doesn't really "explore" these subjects as a philosophical discussion, he just throws it into the narration haphazardly. It's dull and off-putting, especially in contrast to the excellent exploration of so many other topics like the actual symptoms of trauma and depression, which are expertly done (particularly the "triggers" that launch each character into their respective stress reactions, and the consistency of how the stress reactions play out). It's like you have a large, beautifully crafted painting in front of you, but here and there there's just a bunch of squiggles like a toddler decided to play with crayons on it.
I struggle to imagine how hard one would have to misread the game to think that Sensei or Sensei's actions are okay or good.
I am glad that you do, and I hope that everyone else does as well.