I don't think so. Or at least not at the cost of inhibiting discussion. I don't have any answers, and as the article discussed, you can't design a reputation scheme in a vacuum - you need to define your goals and align the incentives with them.

That said, it seems to me that sites like HN vastly over-reward early posters to popular threads. On the other hand, this is only a bug in so far that it leads to problematic behavior. I don't see people taking advantage of it (yet). I'm more concerned with the problem of under-rewarding late, thoughtful replies. I think this is a critical problem with the Stack Exchange (StackOverflow) platform.

The question is how can u get people to re-read the comments page for new comments? Maybe something like a "(5 new comments)" next to the comments link might work??

Metafilter does that, and I think that helps people continue a discussion that they are interested in, regardless of its effect on "reputation". HN does a similar thing with the "threads" link, but it only helps for conversations the user is active in (to encourage involvement?).

My thinking on late (and hence low-exposure) contributions is more along the lines of weighting. If 10 people read a comment and 5 upvote it, it should be rewarded similarly to a comment with 100 reads and 50 upvotes.