I just wrote a long explanation of how we approach the question of flags on stories like this: >>39161344 . If you read that and still have a question that isn't answered there, I'd be happy to hear it.
If you do read it, you'll notice that one factor is whether there has been a major thread about the topic recently. That's important here because the current enormous thread isn't even 2 days old. HN can't handle a major discussion about this topic very often. So while I've turned off the flags, I don't think another story about this topic should be on the front page yet.
If it helps at all, before I saw your comment I was just responding (by email) to someone asking why >>39160743 was flagged, and I answered the same way: that is, (1) I turned off the flags, but also (2) explained why HN can't have another frontpage thread about this two days after the last one.
I know a pair of cases is a small sample but I hope it can count as a sign of how we try to be even-handed. I've learned the hard way that it's simply impossible to avoid perceptions and accusations of bias on divisive topics; even the most neutral moderation is going to generate such perceptions (actually it's worse than that—it's going to generate more). I'm not claiming to be at that level but I can tell you for sure that we do work hard at being even-handed.