I don't know how Joss can say that his Alliance wasn't villainous (to sidestep the metaphysics of 'evil'). We didn't just see the Alliance from the perspective of the Serenity crew; there were scenes with only Alliance personel interacting, and what we see of them then is altogether in keeping with the callous and totalitarian picture that Mal likes to paint. Most every institution and individual encountered is corrupt, venal, motivated by self-interest, blithe disregard for human life, blindly applies a harsh notion of justice, and generally cares for nothing but their own comfort and advancement. Even a seemingly decent fellow like Mr. Tam was willing to sacrifice his children to maintain his social standing, never mind save his own hide; Alliance culture appears to be one of pure egotism. And then there's waging war for no apparent reason (certainly not humanitarian, given what is permitted under Alliance rule) other than the application of power and control, torturing little girls to turn them into assassins, performing dangerous medical experiments on an entire planet's worth of people then unleashing a bloody swathe of murder to cover it up, etc. The Alliance is not terribly nuanced, nor is it ethically neutral.
Really, one way of looking at Firefly is like a right-wing civil war: don't-tread-on-me libertarians versus interventionist, authoritarian neocons. And although the show's nominal hero clearly belongs to one camp, just as it wasn't shy about the excesses of government, nor was the show shy about illustrating the brutality of life without government. If there's no body politic to make the rules, then the guy without the most money or the biggest gun makes the rules.
Fictitiously yours, Trent Roman