Hmmm, both options do seem to have their pros and cons in the current layout of the comment system. You may want to keep displaying comments without points but also try splitting the comment section into two parallel parts: A "Top Comments" column on the left side and a "New Comments" column on the right. This will highlight newer comments at the top longer and may encourage more readers to comment and reply to those while still showcasing the top comments of a story on the opposing left side for those who wish to skim real quick.