Before jumping to the "Them two would be better if they're seperated," I stand by my opinion of them should be more open to each other rather than getting split again.
Ofcourse we already see the fact that Aya's disappearance really traumatized Koto to the point she kept that image of 14-yo Aya in her heart all these years, she then became numb to romantic feelings and can't reciprocate properly.
IMO, although they are living together, she's still in Denial stage of Aya being back for real and the fear of losing her again makes Koto being so overly protective and obsessed with Aya and I think that's OK. Let it be the reason for her to vent and have a happy ending with Aya even if it turns out just to be Tanabata magic shroom.
I am quite resonate with Koto about this because I also experienced almost the same thing... except I don't get my second chance.