Agree with you here. HN users can have some well thought-out and nuanced takes on political issues that span the political spectrum†, but the flamewars are often some of the worst I've seen as well. It's unfortunate because I can't think of anywhere on the internet that has better potential for reasoned political discourse. The only other place is Reddit, and the subreddits there are strictly echo chambers for your own preformed opinion.
† Funnily enough, I've seen flagged accusations that HN users are both too conservative and too liberal; too libertarian and too socialist.
I don't think HN mods operate as conservative or liberal (although curiosity is an extremely liberal cause), but I think they will come to understand the cost of neutrality.
If anything I think they have not fully confronted the paradox of intolerance or realized that the times are different than they were in the last 30 years of internet flame wars. In the past when Godwin's law and flame wars were the rule of every forum, there weren't historians at prestigious universities who studied the holocaust/fascism warning us that fascism is happening here in America right now.