The mechanics aren't completely clear still. Can she reverse the process? Does releasing a soul actually do anything?
In practice, it sounds like she's either killing or gemming them, and then retaining some vestige for her own convenience. Which, while disturbing, is hard to condemn unconditionally given the lack of incarceration options for violent meguca criminals. Sabrina herself is aware that she might need to use Niko's freezer if all other options are exhausted, so our moral highground isn't quite so high here.
What is concerning is that she seems to regard what she's doing not as an unpleasant necessity, but as justice being served properly. She's satisfied with condemning her enemies to eternal servitude. That's fundamentally incompatible with how we do things.
I don't think it's a good idea to look at this and go "She's evil, gem her!", but just asking her to stop probably isn't enough.