I think the Overwatch story does present killing the bad guy as morally wrong. The story implies the push to disband Overwatch came from general public outrage due to Overwatch acting without regard for law, not due to that one guy’s connections specifically. It was also presented as the nail in the coffin: Overwatch had been behaving increasingly ethically dubiously after the threat they originally formed to combat was resolved. It’s part of a larger theme in the story: if a group is well intentioned, but their primary tool is violence, does that group have a legitimate role in pushing for the greater good?