there is a fic in QQ called Predatory where the MC fixed Riley by erasing her memories until she was back to 6 years old, they then put themselves in a simulation(that only lasted a few minutes in real time) where they raised Riley until she was 12 while slowly telling her who she really was and what happened over years in the simulation.There was some heavy discussion regarding Riley and the Slaughterhouse Nine. I'm not going to reopen that, but what I will say is the challenge of rehabilitating Riley is severely undersold in most fics. Riley isn't six anymore, she's twelve. She's spend half of her life doing horrible things with the Slaughterhouse Nine. Even setting aside Jack's telepath power, she's had to build a mindset that allowed her to function in that environment. That's not something she's just going to snap out of. In canon it took Contessa's interference and two years of personal growth to begin to break free, and even then she still launched the Slaughterhouse 9000 before turning around. Just taking her away from Jack isn't going to snap her out of her mindset, and it's very hard to help someone who doesn't want to change. Riley's ability to function is based on the mentality she built up as a member of the Nine. The process of breaking that down in painful and devastating and without the advantage of the specific circumstances afforded by canon and the PtV is likely to be very messy.
Someone wanting to 'save' Riley has their work cut out for them. It is also a very dangerous prospect, and if even one innocent person gets hurt during the process you have to call the entire endeavor into question. Most people can't hope to effectively contain Riley long enough to have any hope of making progress. Joe can, and Joe is probably one of the few people who could counter her well enough to actually say there is no chance she will hurt anyone else. It will still be a nightmarish process to try to walk her back from her current mindset, but it would be possible. What I meant with my earlier statements is that Joe is likely to focus on helping Bonesaw's victims before he took on the monster of a task that is Riley's psychology. At the very least those people would want help and wouldn't be fighting him every step of the way. Also, Joe does not need her. He already is beyond her in terms of medicine and cybernetics. Joe neither wants nor needs Bonesaw on his team. If he does save Riley her future isn't membership in the Celestial Forge, it's proper medication and intuitional care until she can handle society again