The Alliance wanted to make the world a better place, to do away with violence as a part of human nature. That’s why the Operative is loyal to them: his terrible deeds will help to bring about a world in which there will be no more terrible deeds. The ends justify the means.
This is all classic fear of socialism and the state stuff. And underlying it all is the dichotomy between the view of human nature as fixed and immutable - the Christian view of man as inherently sinful - as espoused by Mal on more than one occasion, and the humanist, progressivist view of man - in short, the view held by meddlers of all kinds - as if not perfectible, then improvable.
The Alliance then covers up the horrible results of that project and leave the Reavers produced from it to rape the people of the outlying planets to death. The Alliance also authorises agents to kill everyone involved in, or even aware of, events such as the above. Those events are horrifying enough that even one of those agents becomes disillusioned with them. To be fair, many such things have been claimed about the United States government, but importantly they haven’t actually done them.
The Alliance and the Reavers sounds pretty much like the history of the United States in kindling the flames of Islamic fundamentalism which it is now trying to stamp out, except that the Alliance had rather nobler intent than merely opposing communism and the nationalisation of the oil fields in the region. And of course the history of the US government experimenting on its own citizens and those of other nations is well documented.
In any case one could’ve as easily used the United Kingdom as an example, except that Firefly is an American show deeply stepped in American values and symbols. The old west as the last frontier of the rugged individualist and so on. So: US it is.