The idea is that faith and self-deception are bad, while truth and rationality are good. So we reward good behavior and punish bad behavior.

There's an implicit premise here that the punishment works to discourage the bad behavior. Your argument for this premise is to make an analogy with the gay-rights movement:

How did the gay movement make so much progress in so little time? Was it by engaging in gentle, respectful debate with their opponents? Of course not. They just pointed out the obvious repeatedly: Those people are intolerant bigots.

That is not my sense of how the gay-rights movement succeeded at all. As I see it, they did it by gaining the sympathy of enough of the right people. This, in turn, they did by making their humanity evident. And this they did by having high-status, sympathetic representatives.

Now, once your group is already high-status, you can use scorn to squelch opposition. If you're high-status, people will want to affiliate with you, and they'll read your scorn as a signal that they can affiliate with you by helping to squelch your opposition.

Personally, I'd say that that trick is a dishonest manipulation, because it's not truth-tracking. It depends only on having high status, not on being right. But, more pragmatically, it only works if you already have the high status. Otherwise, it backfires. People read your scorn as a signal to affiliate with your opponents.

Before homosexuals had sufficiently high status, any scorn they showed hampered their progress. But I grant that they eventually gained enough status so that the scorn trick could work. Sam Harris does not appear to me to have reached that level.