Shadow Stalker - She wasn't kept around because she's useful against Endbringers. She isn't. Look at that scene again. She's forced to get too close and she gets creamed. She's super vulnerable to energy in her shadow state (nix Behemoth), can't really close in vs. a fast or mobile target (nix Leviathan for the most part, Simurgh), is emotionally imbalanced (nix Simurgh) and doesn't do any meaningful damage.
People don't generally know about her vigilante background (she kept to the shadows, hyuk hyuk) and the info & reality about her personality didn't come out until she was already on the team. It's hard to unseat a crook-turned-cape once they're on board, because then you run the risk that the public discovers you're bringing less than savory types on board. Besides, in the PRT's view, she was more or less playing ball. Getting therapy, using tranq darts, attending patrols (if alone), attending her track team, and going out to movies with her best friend. If something came up at school, it was generally seen as a bump in the road to recovery. This is why she was as pissed as she was over the meeting at the school where everything came up. It straight up overturned her act. In a calmer situation, if things hadn't gone shit-sideways, stuff would have gone through and things would have changed. Not enough, but they would have.
If Taylor had pushed and pushed and pushed (or if Taylor had joined the team and made an issue of it), maybe something would have happened, but even then... what do you do? It goes back to the question of how problematic it is to get rid of troublesome recruits. Sophia stays on the team in an official capacity, makes appearances, but generally it's for show, and she isn't allowed to patrol anymore (at which point she gets restless and snaps, which the PRT may or may not anticipate, depending on what's on the table).
