We condemn the activities of an organization (moral condemnation) but pursue and punish its members (legal sentence) so, at the end, it serve the same purpose: to get rid of it., right?!
Well, if there was really no charge pending against any members of the Val Jean's crew, I don't think that the Federation - via its armed component = Starfleet - would have deployed as means to trace them (sending a spy, Tuvok, then a vessel, Voyager,
an Intrepid-class starship, just out of the factory), to track down a Maquis ship in the Badlands. Plus, I remind you that as well Tom Paris as some Chakotay and B'Elena's knowledges still alive, found themselves in penal colonies and prisons of the Federation after being caught for their implications in the Maquis (cf to Caretaker & Hunters). So no, serious charges existed and according to some declarations from Starfleet Command in s5 or 6 via a video message, Janeway will be challenged to make her friends being out of the woods, even partially! Indeed, although admirals know perfectly the situation: that Janeway was forced to include Val Jean's rebels among her own crew and that thaks to their active collaboration, Voyager still flies), they still consider Chakotay and his friends as Maquis with all that implies. What isn't a good sign. In short!