There is no speculation needed as to the final portrayal of the Alliance: It is purely evil. Even its sincere proponents will be converted to the values of the Independents as embodied in the Big Damn Heroes. All schemes to improve humanity are vile impostures, and the diabolical effort to deny Nature/God will raise up demons in human form. It appears the Browncoats find these profound truths to be rich nourishment for the spirit.
This is totally wrong. Whedon has said in interviews that the Alliance isn't evil, it isn't Star Wars' empire. There are evil elements within it but he compared it to elements within the CIA or FBI who have been involved in dodgy activities. This doesn't, he reasons, make the whole USA an evil empire.
He has also said that Mal's views aren't his own and that if he met Mal, they probably wouldn't get on. Whedon is a moderate liberal, IIRC and he's compared Reynolds to an anti-government liberterian.
He has also been at pains to stress that while the Browncoats in FF were, like the confederacy, on the losing side of a civil war, they were not pro-slavery. The US civil war analogy is not an exact one.