I'll say this, as my last statement really didn't address your issue with it. But I don't think I can, or even should change your mind because you are right, it is kinda fucked up.
But I think she should be kept around for the mc to realize how bad his power can be, if he loses control of it. Whether he can or will restore her some semblance of her old self, might be irrelevant. As it's a contestant reminder of what unchecked power can do.
My view on keeping her around is also to do with her sister, if she was killed her sister would be left to live on the kindness of strangers. So as much she is a robot now, at least her sister can still enjoy her company. But I realize it somewhat hollow, but I don't like the idea of leave her to fend for herself.
The game doesn't feel like some sort of a dark story where tragedy is at every corner, and it's possible that there will come a point where your really will be able to fix you mistake.
I hope I made more sense with my current view on the subject, and explain my self better.