Conflating Mal's perspective with Whedon's is misleading. From
Joss Whedon: Conversations:
p68 said:
"Mal's politics are very reactionary and 'Big government is bad' and 'Don't interfere with my life,'"" Whedon explains. "And sometimes he's wrong—because sometimes the Alliance is America, this beautiful shining light of democracy. But sometimes the Alliance is America in Vietnam: we have a lot of petty politics, we are way out of our league and we have no right to control these people. And yet! Sometimes the Allience is America in Nazi Germany. And Mal can't see that, because he was a Vietnamese."
and
p68 said:
"Whatever I may think of him politically, [Mal's] a guy who looks into the void and sees nothing but the void—and ways there is no moral structure, there is no help, no one's coming, no one gets it, I have to to do it."
and
p110 said:
"Mal is somebody that I knew, as I created him, I would not get along with. I don't think we have the same politics. But that's sort of the point. I mean, if the movie's about anything, it's about the right to be wrong. It's about the messiness of people. And if you try to eradicate that, you eradicate them."
and
p113 said:
"The political statement that Serenity makes is very blatant—but it can be embraced by someone who's extremely conservative or extremely liberal. That's not the point. The point is that it's a personal statement. [...] And with the show, the idea was to have as many points of view as possible. The reason I made the Alliance a generally benign, enlightened society was so that I could engage these people in a debate about it."
So, to me is sounds like Whedon is aware that politics affect real people. Even when the solutions are generally good, it's never an unalloyed good. And, conversely, a perfect solution will never fit real people, because real people are messy.
Whedon certainly doesn't sound like he personally believes government (even big government) is inherently the Big Bad. It's more complicated than that, and so are the solutions.
That's one of my problems with Libertarianism, because it offers a simple solutions that claims "government is the problem, individuals are the solution." You know what's the biggest problem with government? People. You know what can turn a corrupt government around when all else fails? People.
Same with corporations, churches, charities, the military and the school board. All organizations are affected by human nature, so they are all flawed and corruptible, just as we are as individuals. Unless you outlaw both organizations and the amassing of power (including wealth), corruption and the abuse of power will be things we are always fighting against.
That doesn't mean we shouldn't try to structure things to encourage transparency and accountability and to discourage corruption and abuses of power. We should try to optimize what we can... but keeping in mind that there are limits and that our own human nature limits what's workable.