You're not going to stop giving them the benefit of a doubt after they went and engaged in a war of aggression against worlds that just wanted to stay independent? The Alliance does not have a democratic mandate to govern the Rim worlds. You might as well say that you're not going to stop giving Nazi Germany the benefit of a doubt after they've gone and conquered Poland in the name of greater Lebenstraum.
As I understand it, Firefly was primarily intended to be a metaphor for the American Civil War.
You are mistaken. Some of the concepts and imagery were inspired by the American Civil War, but it wasn't a strict metaphor or allegory for it.
In that respect, you can also argue that the Union did not have a democratic mandate to govern the southern states. Or rather, the southern states did consent to being governed by the Union when the United States was 1st formed. However, that consent was revoked when the south decided to form the Confederacy.
I don't think you can fairly or accurately argue that the U.S. did or did not have a democratic mandate to govern the South, because 39% of the South's population was enslaved -- meaning that 39% of the South's inhabitants didn't get a say when it seceded.
As has been said, many of the transgressions perpetrated by the Alliance have also been perpetrated by the United States at some point,
And as I noted, it's not the presence of any one or two abuses of power, but the systematic combination of all of them occurring in close conjunction with one-another.
No government is trustworthy. But neither is any entire country "good" or "evil" either. While the Alliance government may have had evil intentions, there were undoubtedly good people in the Alliance. Similarly, I think there were good people in the Galactic Empire in Star Wars as well. Remember, Princess Leia was a member of the Imperial Senate, so they couldn't have been all bad. Plus, the Empire was full of ordinary working stiffs who were just trying to live their daily lives.
Agreed; even in the most tyrannical of countries, there are good people and normal folk who just want to live their lives in peace.