The comments on HN aren't perfect, but they're far from bad when compared to other sites of this nature. There has been a downwards trend most probably due to the increasing popularity of HN. A response is warranted. However, this system has the potential to silence a lot of high quality comments on any threads that aren't on the front-page for an extended period of time. Thus, you get a feedback loop. Good posts require quality discussion to stay on top, but must stay on top to get quality discussion going with this added approval lag.
I think you should ease these changes in as conservatively and gradually as possible. For example, apply it only to the top page at first, and reduce the number of endorsements required for display to 1. You might also consider merely greying out comments that have not yet been endorsed, as currently happens to down-voted comments. Another option would be to apply the endorsement system only after threads have reached a certain age so as to jump-start discussions. Additionally, I would recommend that authors of a parent post should be able to see all child posts regardless of their karma. Below, Babuskov raised the point that the endorsement system will obstruct useful back-and-forth discussions between sub-kilokarma users in buried threads that often takes the place of a private messaging system on HN. This would fix that more effectively than merely reducing the endorsement requirement.
You should not entertain any illusions that you can flip the switch and watch this system work perfectly, and that you will therefore be able to avoid confusing people with many changes over a lengthy period of time. Tweaking will almost certainly be required.