I'm going to give my opinion on this matter. Personally I'm NTR neutral: I enjoy both good NTR games like The King of Summer and the countless harem games in this forum. So I am not affected, at least initially, by the heated passions that NTR games generate in others. The only thing I ask is to know from the first moment what kind of game I am playing. I don't like to play a supposed harem game and, two years and several updates later, suddenly find out that one of the LI is a prostitute before, during and after having met the main character.
About lesbian sex in a harem game, I personally don't mind it, although I would prefer to avoid it. The more time is spent on this kind of scenes, the less time is spent on what is really important: the MC and his harem. And above all, the main plot, which is what's really important. Lesbian sex in a threesome or more with the MC? Although some people don't like it, I personally accept it. What is not recommended is to develop 100% lesbian sex scenes. The developer wastes time and resources on something that a harem game player would never play. I would never play a lesbian sex game, and for that same reason I would not like to see lesbian sex scenes.
Another thing is what people consider “harem” and “lesbian sex”. This gives for many explanations, which for that reason I prefer not to explain. There are people who consider sex between two women in a threesome with a man lesbian sex, even if for example the man is penetrating a woman while she is eating the pussy of the other woman.
The problem of developing a game with two protagonists and therefore two harems is, in addition to what Juerhullycin has said, everything is duplicated. Normal, because in the end you are not developing one game, but two. Even excellent games like Stormside, with a single protagonist but with three different branches (love, submissive, slave), in the end it is as if you were developing 3 games, and that is very noticeable in the development of the game and the update speed.
Your game reminds me of another game whose name I don't remember (I've played so many...) made using Ren'py and Koikatsu. A brother and sister pair, both main characters, go to a new city, famous for its high sexuality content. Normal, as there are succubi and sex magic in it. While the brother has sex with many women, the sister... too. She becomes a succubus and has sex with both men and women. The developer said that his game was harem. But he commented that the siblings would not have sex, which pissed off incest lovers. And seeing how the sister had sex with random men and women pissed them off even more. I don't know how you are going to develop your game, but I have the feeling that something similar is going to happen to your game.
In short, on the one hand it's your game: develop it as you want. On the other hand, if you want to make a harem game, take into account the opinions of players who only like 100% harem games. And in this kind of games, for this kind of players, lesbian sex is not only superfluous, but it is not part of a harem game.