If the article were garden-variety flamebait then it would be a different story (no pun intended) – but this was such a clear case of the opposite.
The best thing is to give us a heads-up at [email protected]. That could be either "hey, there's a really good article getting unfairly flagged" (a user did that last night and it was extremely helpful) or it could be "hey, there's a really good article getting a lot of flamewar comments". Actually it could also simply be "hey, there's a really good article that hasn't gotten any attention yet". (People often send those for their own articles, but that's a little less noble and not what I'm talking about here.)
You can see the common denominator there: "a really good article". There aren't very many of those. Just as the most important thing for startup investors is not to miss the best startups, the most important thing for HN is not to miss the best articles.
A standard version that I often see is when articles get sunk by shitty comments are when the author is controversial. The negative comments are focusing on the author, and often that dominated the article comments until the article get flagged to death. Fair? No. It is however a pattern that keep repeating itself.
I don't recognize this bit though: "Not being able to use the flag feature when a article is being used as fuel for culture war". That doesn't sound like what I said and certainly isn't what I meant. Edit: oh, I see what you mean - "being used as fuel for culture war" is your rephrasing of what I described as "shitty comments". Don't take this absolutely, though. The median case is that both the article and the comments are garden-variety culture war; those are legit to flag. I'm just saying that you shouldn't flag indiscriminately. We want some discernment when an article clears, let's say, the 95th percentile of thoughtfulness.
At this time the first 50% of the comment page does not discuss gender so it clearly turned out right, but they were posted after the dead comments. If a fresh article has the majority of comments being people warring about gender then the option given to users is either to ignore the war, flag it, or engage in the discussion. Having seen that multiple times it is often easier and uses less time and energy to simply flag the article regardless of how great the article actually is. The flag would not be a comment about the quality of the article, but rather the climate and culture for which it was posted in.
Dang, is this a problem?