Here's the top of a conversation I had with him, starting with me:

  Thanks for the thought out response. I agreed with just about everything you said, which makes this whole situation that much more frustrating. On one side, you're right and you're trying to create substantive discussion, which their sensationalist reporting often rubs against. On the other hand, [dead] in its current state is neither informative nor allows for substantive conversation about why it's [dead]. Ironically, the action of [dead]'ing looks like a malicious response from you and your colleagues -- something that's still hard for me to shake, especially considering who owns HN and who's within its network. Or at the very least, it looks malicious in the face of potentially simple UX changes.

His response:

  Yes, I hear those frustrations and they all make sense. I'm afraid I'm pessimistic, though (having been at this job for many years) about the possibility of a fuller explanation ever clearing up these perceptions—for example the perception about "who owns HN and who's within its network" being the main factor in what gets marked as [dead] on the site. In my experience, (some) people are going to believe that, regardless of anything we say or do. A lot of people on the internet are primed to perceive maliciousness and, sadly, I don't think we have the power to change that.
 
  I also don't think it's possible to "promote substantive discussion about why [a post' is dead" because that sort of meta-talk invariably becomes bogged down and self-referential. In my experience, such discussions don't lead anywhere productive, they just generate more and more of the same. 

  The moderation burden such meta-discussions impose is high, because if we don't answer and explain, our absence gets taken to mean that we're hiding something and/or that whatever people are accusing us of must be true. That's potentially disastrous for HN because it means that those moderation resources get sucked away from things that matter more for the quality of the site.

  But I don't want to come across as too dismissive! I appreciate your openness and your suggestions and will think further about them.