If the rape that appears at the end of the intro is carried out, no fan of the harem genre will touch the game, not even with a stick.
Either you make all scenes where the MC is not involved avoidable (i.e. they don't happen), or you're going to have a very difficult time selling the game to harem and vanilla players. Raping one of the LIs is a terribly stupid idea in a harem game because it kicks that part of the audience out of the game. Maybe you attract a few fans of NTR and the like, but you lose the biggest part of the audience.