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.