And although there are ways to improve the actual implementation of the system, I still think it is fundamentally flawed for a few reasons.
First, any system in which a comment is assumed to be spam or trash until proven otherwise will produce less meaningful discussion. Maybe most of the good comments will be filtered through; but some will invariably be missed, and people with valid ideas will not have their comments seen by anyone. Moreover, from my understanding, the HN user base is primarily in North America. (I could be wrong.) If this is true, won't users in other countries be disproportionately affected by this kind of oversight because there are simply fewer high-karma users in the rest of the world?
This is fundamentally a debate over whether HN should have 50% fewer good comments and 100% fewer bad ones, or whether we should just get everything. I believe that latter.
Second, this program places excess responsibility in the hands of high-karma users. HN is now moving from a passive system (eg. one where everything is visible and the best stuff gets voted to the top), to one where every comment must be scrutinized and evaluated just to be visible. Logistically, I don't see how this works. Users with over 1000 karma are rare. From what I've seen they are less than 5% of the total HN user base. This minority is now going to be responsible for evaluating every single comment?! I truly do not see the small number of high-karma users on HN being able to sort through every comment. Many, many comments will be missed or ignored.
Overall, I believe that any effort to stop spam on HN should be given consideration, but this system poses substantial logistical problems and will, in all likelihood, hurt the community.