It's still been barely any time since she left, so it's tough to say what the author has in store. Maybe her being constantly present would have somehow impeded what he wanted to focus on next. Maybe her still being casually around would have subverted what he wanted to tell with her leaving.
People leave companies and never come back all the time, after all, and maybe he wanted to show the experience of the ones left behind, and how they deal with losing a close colleague, a role model, an instructor. There's already been a bit of that with Momiji seeking out Hotaru; that's something she wouldn't have been likely to do if Yagami was still around for her to learn from.
So I wouldn't be so quick to label it entirely subtractive. It would only be subtractive if the characters are static and unchanging, which has never been the case in New Game.