I hope that by choosing to get rid of your alter ego, it will not be a purely NTR path, and that that splits into the NTR path and also the "pure love" path (Where you can choose if you want to intervene with other characters advances against your harem members, or if you are "too weak" to do so). If there is only a choice between NTR and being a dominating alpha dick, then half of the game won't be viable for me (Not a fan of either, but I do like romance and the soft method of getting into a woman's pants).
Not sure if you've played all the way through, but the way it seems to work is this; the MC was very insecure, very indecisive, too afraid/cautious to ever act on his desires or be proactive about making changes in his life. He mostly just kept his head down and kept on keeping on, burying his emotions/desires/fantasies way down deep inside. The alter ego is basically everything he's ever buried coming out to play all at once. So his darkest desires on crack. But as time goes on, the idea seems to be that everything returns to the mean. The alter ego mellows out and is capable of showing empathy and care, and the original personality gains confidence and a willingness to fight for what he wants (starting by admitting that he DOES, in fact, want things).
Which is sort of the problem with what you want for the character. Without the alter ego he wouldn't go through that development, and thus it wouldn't really make sense for him all of a sudden to have the balls to just.....handle things. If he could do that so easily, the alter ago wouldn't even exist. And if the alter ego is taken away too soon, before he undergoes that development, the logical conclusion of that arc is his personality won't change, and he'll just end up watching helplessly while everything he COULD have had is taken away.
Personally, I think it'll probably end up the way you want by the end of the story, with the MC and the alter ego fully integrating, and him being a loving partner to his harem of beauties........albeit one with a dominant side if he chooses to indulge it. But that'll probably be end-game stuff.