For me, it wasn't so much that I 'forgave' her for anything she did, I do know that she's done evil things and killed innocent people, but as her story developed I slowly learned what I already expected, that this was about more than her will to do evil things...
I think the big turning point was when we are told that she *has to be at war* in order for her to work. Her powers just aren't the same, nor does her health, if she is not at war. That didn't make me 'forgive' her, but it made me understand her better in a way that we haven't come to understand any other character, just like FairyGodfeather said.
Think about it for a moment, she would have been dead earlier on from radiation if she hand't been stalking your every move, and planning all those things that she did.
I'm not justifying her actions, I'm saying I passed to understand her, which matters considerably. With Black Magic, it wasn't so, as she felt crazy just because, no reason whatsoever (that I could reason satisfactorily). Prodigal was conditioned from birth to have an aggressive nature over other living things, *part of her* wasn't because she wanted to, but because this is the way she was born, the way her powers aligned with her.
She didn't choose her powers, just as we didn't choose ours, but as it turns out, we have very useful powers that don't require us to be at war with anything. Living like that was the only thing she learned.
Finally, I do not think she, although conditioned to be the way she was, truly liked to be evil, or murderous, or whatever. I think she preferred to be good, and I wanted to help her achieve that, romance or not. I would gladly sacrifice a part of me to help her stay alive and prove her own nature wrong, damn the social stigma, but I have no complains from the outcome--Whatever way, positive or negative, was just perfect, just as it was supposed to be, no matter how much I wished for it to be different, for such is life.