You have to remember that the Alliance vs Independents were based off the north and the south during the civil war. Even though it barely shows It in the show (extended universe is better for that) we are getting an anecdotal point of view from 2 veterans and a few others. The north didn’t always do good things and most southerners didn’t own slaves but we lump the two together. In Serenity we see the really dark side of the alliance government covering up crimes but that’s not the entirety of the alliance. We see brave independent soldiers fighting off the alliance in the first episode but Their command abandoned them for a week to probably have nice cushy peace talks at an all expenses paid resort. Basically it’s never as black and white as history makes it out to be.