Joss Whedon spoke to this specific question in a series of interviews in 2011. To cut a long story short, not only is the Alliance emphatically not evil, they're actually best characterised as benign and culturally enlightened (offering free healthcare, universal suffrage, free high quality education and excellent policing):
Whedon: ...And people are always like, "They're fighting an evil empire!" And I'm like, "Well, it's not really an evil empire." The
trick was always to create something that was complex enough that you
could bring some debate to it—that it wasn't black-and-white. It
wasn't, "If we hit this porthole in the Death Star, everything will be
fine!" It was messier than that, and the messiest thing is that the
government is basically benign. It's the most advanced culturally. . .
One of the show's enduring charms is that from a certain perspective the most morally questionable of the Alliance's actions (the Unification War, the Pacification of Miranda and the deployment of the Operative) are arguably in the best interests of the population. In the real world, there are invariably shades of grey:
JW: Evil doesn't come in saying, [breathes heavily, Darth Vader-style], "It's your faaather." Generally speaking, it's a lot
more nebulous. In fact, it usually isn't evil so much as it is a lot
of people overthinking things until they find themselves caught in an
Notably, even the Alliance's own man can see the obvious connection (but rejects it);
THE OPERATIVE : He's not the plucky hero. The Alliance isn't some evil empire. This isn't the grand arena.