Of course that leaves the harder problem that some of those threads are flamewars rather than civil conversations, as the guidelines call for. But fortunately that's not always true.
Thanks again for sharing your learnings. Unsurprisingly I have some thoughts of my own, but first I'm curious about what others have learned ...
But why do you think it's uncharitable? People who say they "prefer meritocracy" are in fact taking an anti-diversity position. Maybe they don't understand it's anti-diversity, in which case pointing it out may encourage them to think more about it and understand why. Or maybe they don't care, in which case they certainly wouldn't take it as a moral judgement.
I don't think it's uncharitable for people whose explicit, self-proclaimed position is that diversity makes things worse than homogeneity.
In terms of hot-button-topic stories getting buried, it's not just flagging - the flame war detection logic also plays a role. On diversity stories, for example, once they reach the front page we often see a large number of strongly worded (but clearly legitimate) anti-diversity posts. When people reply, heavy discussion ensues; and in any case, there's often a lot of piling on in agreement. Pretty soon the post is back to page 3 or 4. Of course there's the option of not replying, but leaving the anti-diversity viewpoint unchallenged strongly reinforces the stereotype of HN as a place that's hostile to diversity. So right now there isn't any good answer.