We've found the best approach is to answer questions openly, let the answer persuade those who find it persuasive, and not chase diminishing returns down the long tail of objections. That approach only works if the community finds it persuasive—otherwise hellfire would rain on our heads—but empirically, the bulk of the community does. I think most people understand that it isn't in our interests to lie about how we administer HN. The good faith of the community is the only value that HN has. Why would we risk that, and for what?
Edit: actually this is kind of an interesting example to work through. Let's assume the OP is authentic, everything in it is true, and that it's an important new development (what I called SNI here yesterday: https://news.ycombinator.com/item?id=38357788). How would it help YC if we suppressed it on HN? It would only make the HN threads less interesting, since (by hypothesis) the real story wouldn't be getting discussed. People would leave HN in search of interesting discussion elsewhere. That would make HN less valuable. Meanwhile, being an important story, it would end up getting attention everywhere else, people would keep posting it to HN, and we'd have to keep suppressing it. We'd end up in a fight with the community, a fight we'd be sure to lose. This is a way to destroy HN, not squeeze extra value out of it!
My guess is that users are flagging this story because of some combo of: they doubt that it's authentic; they doubt that its claims are true; and/or they don't think the claims are SNI* even if they are true. Perhaps some are thinking "oh my god, not another open letter—I'm so sick of this saga..."
I get that you do consider it true and important, but so far, the community verdict is against your view. If the flaggers are wrong, they story will get some confirmatory reporting soon enough. I'd be surprised if a few eager reporters aren't already looking into it. If they find some there there, we'll be able to have a discussion soon enough. In the meantime, this story hasn't yet cleared the bar for SNI—especially since there are dozens of articles being posted about this topic right now.
* Significant New Information - see https://news.ycombinator.com/item?id=38357788 etc.