But see now you're forgetting who put those words in Badger's mouth- Joss Whedon and the writers. This was the beginning of the pilot episode where characters are being developed for the viewer to better understand. Badger was merely a plot device to sum up Mal's personality in a quick couple of lines regarding his lingering attitudes about losing the war. This was so viewers like you and me would understand where Mal was coming from and go on to watch episode 2. This wasn't a point Badger was trying to get across to you, it was a point the writers were trying to get across to you. The "character" Badger said those lines because he got the sense that Mal thought he was better than him- no problem there.
He never saw the ships leave his ass, he looked to the sky and saw thousands of alliance ships flying up it. I doubt he felt abandoned, they were completely outclassed.
He even said he was on the losing side, not the wrong one.
I don't know how you're trying to use the Pax and social conformity to apply to the Browncoats- that makes no sense. Do you think flags in general stand for oppression or something? A flag is not a society, a flag is an idea- an ideology... and I don't know how anybody can watch Firefly and not think that Mal is an idealist.
I'll agree with you he lives for his crew now, but even thats part of the soldier in him. He stands up for Doc and River because they're "crew" -Just like in war he leaves no man behind.
Really I can't believe this is even up for debate, its in almost every episode. Mal hates God because he can't let go of the war. Mal picks fights with Alliance vets every Unification day for fun. Mal says he would rob the goods on the train out from under the noses of the Alliance troops for free. Doc gets his head knocked off by Mal for suggesting he's afraid of the alliance and probably wouldn't mind working for them. In the movie Jane almost fights Mal because of his vendetta, accusing him of letting his feelings for the alliance put all his friends in danger. Inara even pipes up, "this isn't the war Mal"
this is glaringly obvious, I don't get the opposition