Re: libertarian streak etc - no, we're not supposed to take Mal's view as the necessarily correct one. And bear in mind that in the very pilot, we see an Alliance captain, upon hearing what he thinks is a distress call, breaking of pursuit of Serenity to rescue the supposed people in distress. Something Mal & Co. have been counting on. Meaning this is official Alliance policy. So we're not talking about a cliché evil Empire here. (I think Joss said somewhere "the US as seen by the Vietnamese pov", but I can't find the interview; the American Civil War, though, was the original inspiration, he got the idea for the show after having read The Killer Angels on the flight from L.A. to London.)

Also, both Inara and Book, sympathetic characters, supported the Alliance, not the Independents, in the war.