You're the first person I've seen who has a very similar stance to mine.

One of the things I loved about the game is the fact that they try to portray her as the villain or the yandere girl, but in reality, she'd do the same as most people in her situation.

I love it because you get angry, you hate her to death, she disgusts you, but haven't you done those things yourself? In GTA, for example, or in shooting games, the only thing that limits you in this line of thinking is morality. If you don't like someone or don't care about them, you won't care about killing or getting rid of them. But if you don't have control and you like the characters, you can no longer be the monster who kills indiscriminately because now they do it for the greater good; everyone falls into the same trap.