The problem with this system is it actively penalizes use. I see the point of wanting users to have skin in the game, but if I had to give up 2% of my HN "karma" to post this comment, I probably wouldn't do so. If you extrapolate that across all users, you may gain more quality content, but using the site would feel like being punished. And with a social news site, your biggest problem is gaining critical mass. The last thing you should do is discourage use in any way.
Instead of penalizing those things, you should be using them as a metric for measuring site use. Pinterest, for example, would use "repins" as a way to see how much the users are enjoying their experience. Reddit and HN might use upvotes or comments. What you want is as much content as possible and a good sorting method to weed out the best stuff, which is what HN has.
But I could be wrong; we'll have to wait and see.