This phase was surprisingly shocking to me too. I already didn't like Flay Allster much at that time, after that I hated her with a passion. It was an interesting fictional character though.
First time I watched it, I misunderstood Flay's intentions. I feel somewhat more sympathetic to her now, but still, I think she's a horrible, selfish person.
You see, she seems as if she's completely insane and it is trying to push Kira on as a way of torturing/punishing him for being a coordinator. However, I now realize that she's just a stuck-up teen girl in an extraordinary situation, just like the rest of them. However, she is a massive coward. She tries to build a strong relationship with Kira so he will feel compelled to stay near and protect her. It's clear to me she doesn't see Kira as a human being at that point, but rather like a sub-species... or better yet, like a robot. An artificial creation that is greater than humanity, but in the process, became somewhat less human. So, if she has builds a romantic bond with him, she knows he'll push himself to protect her like what she observed with the little girl. Kira as an extremely ethical, humane, and empathetic person, and Flay is a selfish coward who wants to take advantage of it. It's not about being lonely, either. Sai was good as gold to her... but, he couldn't fight in a robot to keep her safe, so she did him dirty.
That being said, I understand how at that point Kira was under extreme pressure and his failure to protect that girl when Yzak blew up the Magic Schoolbus made him feel like his effort was inadequate. (remember, Flay intentionally gave him the flower the girl made for him to remind him of his failure) He really acts out of character after that. Most noticeably, he kills enemy suits with this emotional, almost primal violence in the ensuing desert battle. He snaps out of it after a few days and distances himself from Flay, so I guess he can be somewhat forgiven. But, I do recall Kira's behavior during that period being infuriating, and EXTREMELY out of character.
At least, after watching Destiny, you can appreciate that fact that Kira is flawed. He's basically Jesus in Destiny. Moral to the point that I think his wartime ethical reasoning is flawed. Maybe it's a bit selfish on his part... he would keep his hands clean from blood, and push his burden and responsibility on other people, despite the fact he has the greatest ability to end the war quickly and ethically. And in the process, how many thousands (millions?) of people die because he refuses to fight?
Bonus:
http://kenkoudaa.sakura.ne.jp/page197.html
Click on 逆襲のサイ （Sai's Counterattack) Even if you don't know Japanese, you'll get the joke.
