[spoiler] um...Could we not just have come back for him?

[GrAVit]

Well, she would've had to see Simon-2 suffer after waking up in confusion and learning that they're all doomed. I'm sure she wouldn't have wanted him or herself to experience that, especially because he would've probably started blaming her for everything, just like Simon-3 did.

It's definitely the explanation that makes the most sense, but her angry reaction to Simon-3
after launching the Ark, implies she thought Simon-3 understood the copy concept by now, so if Simon-3 can deal with, why should Simon-2 not be able to?

Well.. it's a copy of Simon himself after all. Giving Simon-3 the choice to decide what to do to Simon-2 would be the correct thing to do. If Catherine insisted on not killing Simon-2, Simon-3 would've definitely questioned that, which is when she would've had to explain that he will technically remain on Pathos-II and that there is no salvation for him. That might have caused Simon-3 to freak out at her like in the ending and not cooperate with her, so that the ARK project would've failed. She probably didn't want to take that risk.