I don’t think they’ve made it the bad guy. It’s still Starfleet. Just Picard and Starfleet disagreed about something 20 years back.Although, I do have to ask, why does every Trek series take Star Fleet and make it the bad guy? We saw it back in TNG, DS9, and STiscovery. For a "utopian vision" of the future, Star Fleet sure likes to go back on its principles.