I guess I can see where you come from. But I also don't think she'd be the "safest" to reform. She'd be the trickiest, tbh, because of how manipulative she is. I think she could very easily trick everypony again and convince them that she's reformed, while hatching a new bigger and better plan in the shadows. That's why I personally think it was the safest idea to keep her contained somewhere where she can't hurt anypony. Again, a bit over the top with her being a kid, but understandable to an extent.

Coming off what you said about Rusty, I will say that I'm genuinely surprised that he, and most of the Pegasi for that matter, didn't actually recognize her. I would think after commiting such a large felony against Equestria that everypony would at least know her face. I guess thats more of the show itself at fault though with a small plothole, rather than the story ¯_(ツ)_/¯