It has been a while since I watched Firefly, but going off memory, in the episode with the sword fight, Inara and Mal are talking because Inara was confused about why he reacted the way he did, after all he always insulted her, and his reply was that he never insulted her only her profession. The impression that I had was that he was violently opposed to people selling themselves to earn a living. Even if it was socially respected and legal. Just because something is socially acceptable and legal, does not make it morally correct.
His problem was with the profession and that it was respected and legal was just another reason to hate the Alliance.