Well, that makes more sense, however, I don't think that negates my original point. She still rejected Cloud on some level.
Oh I agree, I definitely think she did. I think she sort of realizes she was projecting her own desires onto Cloud, she saw something in him specifically because she was looking for something in him.
Even disregarding the fact that Cloud is in a sense, Zack, and that Aeriths feelings for Zack seemingly latched onto Cloud, I think that even without that, Aeriths' attraction to Cloud is still not really natural, or perhaps "normal" is a better word.
I don't think Aerith slowly fell in love with Cloud because of their time together and an appreciation of who he is (how could that be the case when she literally doesn't know who he is).
I think Aerith was looking to fall in love with Cloud, I think that she not only saw Zack in him, but perhaps a way to get over Zack. She wanted him to be someone, and started acting towards him in a way that fit that vision. In a way, she was acting out a fantasy much like Cloud was, and he played the role of her emotional savior, he's her rebound.
I don't think she really thought about it that much of course, I just think that when she saw Cloud, there was simply a conglomeration of emotions there. A wish to relive her time with Zack, a hope that Cloud was like Zack, or somehow even was Zack, a hope that she could get over Zack with this Soldier, a hope that she could fall in love again, etc. And all of that primed her to develop feelings, and be a bit blind to reality, or at least look at it through a colored lens.
But when Cloud attacks her, I think that's a bit of a reality check for her, a lot of those hopes sort of break, there is a realization that that was a big burden to put on someone, especially someone whose not emotionally well. She realizes he's not her savior, and that both of them have kind of been putting on an act, using each other to avoid facing reality.
So while I do think Aerith rejects Cloud at that point, I don't think she rejects Cloud as an individual, I think she rejects the validity of how their feelings for each other came to be, she rejects the process. I think that had she lived, she'd have tried approaching Cloud as if from square one, trying to see him for who he really is, and seeing whether or not she's attracted to that, instead of forcing herself and him into that role a priori.
Even though Aerith talks a lot about wanting to meet the real Cloud, and gives off the impression of "just wanting Cloud to be himself", I fundamentally don't believe her. She has feelings for (Fake)Cloud, which means that she has SOME vision of who she thinks/hopes/wants him to be. Her feelings come first, her desire for him to be himself followed after, which means it's not pure, there is a weight that comes with her push for him to become "himself", which fundamentally skews the goal.
IF Aerith had lived, I think she'd have rejected all her feelings and hopes for Cloud until after he'd become himself again and both of them are able to have an objective look at who the other truly is. But that's just speculation.