That's certainly a possibility. It would show up in HN's metrics. (perhaps not visible to you and I, though)
On the other hand, you might also see more people coming in the door. What if this makes conversation on HN so much better that more people want to get involved?
The one thing that is certain with the new system is that if your comments are abusive, they will probably not get endorsed. Perhaps at first they will (protesting 1k+ karma users) but eventually anyone who is endorsing poor quality comments would likely lose the ability to endorse.
At a minimum, I think this a really interesting experiment.