I've never understood that criticism. The Gems weren't really genocidal or imperialistic. Both of those terms imply the act as "targeted", at least in my mind(less so imperialism but I digress) . They're a galactic alien force bent on extracting every resource they find, and barely even acknowledge other life being so far removed. I'm vegan but even I can't prevent or spare thoughts for life I destroy just by existing and walking down the street, which is what I'd somewhat compare it to. When finally confronted by a force that could match them and share a different morality they showed a willingness to change and learn. Are we supposed to punish people for wanting to change who, I reiterate, had an alien morality? That seems like a lot more interesting topic to handle.

Also real world answer, the show was canceled way too early so who knows how they would have handled "rehabilitation" given proper time.