There is an unreliable narrator happening here. The source of most of the information about the Alliance is from the crew. Notably, Shepard and Inara do not share those views. Zoe and Mal have very strong opinions about the alliance and the Doctor and River help feed that narrative. But the things they don’t say out loud paint a very different picture. I think had the show gone on, the brown coats would gradually have become another villain and Mal would have had to contend with the reality of who he was fighting for.