Various Star Fleet officers have periodically violated Federation rules and guidelines to achieve some ideological goal or moral imperative that cuts across the fleet's stated mission. Like with anything there's limits - Starfleet has its own police, crews can mutiny, eventually you run out of dilithium to gas up your warp drive so you can't go rogue forever. But for a deep space galaxy class vessel, they're regularly stuck making their own decisions under a military autocracy.

The Starfleet Admiralty Problem is a chronic plotline in the series, with admirals routinely engaged in all sorts of corrupt practices and villainous endeavors. Every captain from Kirk to Freeman has to deal with their share of higher ranking officers fucking around and being dumb assholes. Hell, Kirk himself is demoted from Admiral to Captain for going rogue in The Voyage Home.