I'm envisioning a use-case for this would be when say, an article briefly touching on tech interviewing (or with a title about tech-interviewing) is posted, and immediately the top-comment changes the subject to "Boy tech interwiews really grind my gears!" Suddenly everyone wants to vent and the thread is overwhelmed.
One natural reason for this penalty is that a highly-ranked comment brings along all the comments that ride along with it to the top. The most extreme form is when the entire comment page is a single comment-thread.
Alternatively, a flexible proposal is to allow users to choose their sort preference, like they can on reddit.
The fundamental issue here, at least to me, is that the upvote is an "I like this" signal. The instinctive use of an upvote is to see more of what you like. Turns out that what people like is what people already agree with.
Unless you build a strong culture that values the signal/noise ratio (remember that early reddit had much more of "UPVOTE IS NOT A DISAGREE" culture, hivemindy as it was), you're not getting your desired outcome. Worse, if you let in the mobs, it doesn't matter how principled your initial group was as they'll soon be overwhelmed by the crowd. The historical record there is obvious.
I think the only way about this is gate-keeping. You want that culture, you'd better enforce it. If you somehow start with a seed userbase of principled people, you only allow people voting rights once they meet whatever gatekeeping criteria that you've set. I don't think this is that scalable, but smaller more tightly knit communities might be a plus to some.
Actually, I'm wondering if something like this might have a niche out there somewhere. We know that Digg in the old days had the superuser group, and the strength of reddit was it's specialized subreddits. Would a system crossing specialized subs with hierarchical user privileges (viewer/voter/voter_with_grant_privs) be something that could work?
In a way it's sort of evolutionary. People attempt to propagate their own ideas or similar, and remove ideas they dislike from the meme pool, via voting systems.
If you take it to the extreme, a youtube video being posted and everyone having to wait 5 minutes to comment, there is enough people that will see it at 4.30 to have a visceral reaction and post inflammatory comments. You can extend that down to each level of comments.
You can, of course, click on the timestamp and see it anyway, so it's more of a speedbump for folks who don't know all of the details of how the forum works than a true delay, though.
It'd be very interesting to see how a short delay of posting comments on new post would impact this.
Compared to other vote-based sites, HN is very health - but to your point, reflexive, shallow comments are the easiest.