Vanillabros and even others that aren't vanilla only types aren't going to like characters that turn on and murder the MC no matter how much its explained.It's kinda hard to hold it against them for turning into NTR heroines in a hypothetical future where they're made the victims of corruption magic that basically mind controls them into being sluts.
As much as you want to chalk it up to plot devices, they're just going to pass hard on that. Personally I find that aspect disdainful myself. Its a whole different layer of betrayal type stuff I'm turned off by than just becoming a fucktoy for the antagonists.
He also made the point that good NTR should be played against a good existing relationship, so he wants the vanilla route in place first so that people who want a more masochistic approach can build up the sense of losing a meaningful relationship and not just losing a potential one can. At that point you might as well also implement win conditions for people who want to avoid the NTR which gives us the harem vanilla route.
All of this is why I think it'd be better served separating them into different universes and sets of characters. Go all in on harem/vanilla/wolesome etc whatever for one, go in for the NTR and brutal stuff with another set of characters. Simple name and character design swap. Its koikatsu assets for them and a quick tweak to pull off. No need to hold back with either for the content then.Personally I think the best route forward given that it's too late to change the premise into either a pure harem or a pure NTR game would be to compartmentalize the NTR into either a DLC or a sort of spin off with the base game and the NTR content in it.
Its not like people who want the NTR content are harmed by it, unless their entire motivation is obsessing over the characters players who would like a vanilla path end up corrupted/betray the MC. Which is just as obnoxious/petty a reason for wanting NTR as I can think of. Two separate instances, both get the kind of games they'd enjoy, win win.