I think the main difference between B7 and Firefly
is that Blake was actively trying to lead a rebellion against the state, while Mal had already lost his rebellion and was just trying to avoid entanglements with the state.
Also, the B7 Federation was far more oppressive than the Alliance. A lot of people assume the Alliance was a dictatorship, but the intention was that it was just a government, one that was well-intentioned and tried to take care of its people, but that, like any government, had its downside and its corrupt elements. Had the show lasted longer, we would've seen more of its positive side from the perspective of characters like Inara.