You can probably skip all the harem scenes and endings by avoiding all the harem acceptance triggers (double hearts icon) as much as possible. If I'm not mistaken, the love points is a separate level-up system so you should still be able to raise your relationship with the women individually. Also, I've unlocked the rest of the gallery, and unless there were any scenes of a wholesome relationship ending that have been excluded, I'm afraid they just don't exist.
I've realized early on that it's almost impossible to fail with any woman in the game. There are only two routes to your relationship; either she becomes a sex partner or a romantic interest, with the former leading up to a harem ending. It goes to show that the MC was simply written to be likeable regardless of the choices the player makes, which is really my biggest gripe towards the game. IMO there should be choices that will lead to negative consequences otherwise you're just playing a perfect, infallible character, and there's no fun in that.