I'll sing the chorus line of needing to include a shhip of some sort, and add that I'd like to see it run as a pure fantasy - i.e. a ship not a starship. I'd go with it pretty much as Felix proposed - imagine a British Empire spanning the globe starting to fall apart but then for whatever reason re-exerting control. So your rebel's are your carribean islands, african nations, india, australia etc. The only connection to the homeland is the seas and being unobtrusive on 70% of the planets surface is fairly easy.
So the 'Alliance' HQ is a far off continent and the action is set in a distant archipelago where the crew can get mixed up in local politics, trading etc. It turns it all into a bit of the pirate game - but provided you keep the crew and their resources small and they take on the 'illicit trader/smuggler' roles then it shouldn't get out of hand.
Ultimately Mal's crew are too 'small fish' for the Alliance to throw anything serious at them - so give your 'empire' something else to keep them busy - a Blackbeard character, or a rebellious indigineous population that needs to be kept under control and sucks up resources, allowing your party to slip under the radar - provided they don't make themselves and important target of course.
I have to say that I wouldn't throw out the other races of elves, dwarves, halflings etc. - they can help give the feel of drastically different cultures on a small planet.