1) Revert to showing scores for top level comments. This will allow people to know whether the top-of-page responses are well-liked by the community, and how fast this approval drops off as one scans down the page. It will also privilege top level comments, subtly discouraging people from pinning their answer to the current top-of-page comment when it's not really a reply.
2) Keep hiding scores for replies (as it is now). This seems to be increasing civility, and discouraging quick quips. It might even make sense to discount the points internally, giving yet more emphasis to the top level. This emphasis is important because the top level dictates the overall position on the page (things move as blocks). Hiding the response points will also encourage people to vote up threads as a whole, which helps with the case of useful questions which lead to good answers.
3) Now that top-level is emphasized, add a 'fold' to the page. But instead of basing it on number of comments, cut off at a negative point level. As they currently do, downvoted items will migrate toward the bottom, becoming fainter as they go negative. But rather than eventually displaying a fixed negative number (-4), just put it below the fold and only visible with a 'show all' link. This will discourage trolling and piling on, as once a comment is below the fold it's unlikely to attract many additional viewers. And it will encourage others to 'clean up the page' if they feel their vote will have a clear consequence. Starting to fade at 0 and folding at -4 seems like a good start, but one could also fold earlier or even bring new unvoted comments in mid-fade.
I think this hybridized approach would be easy to try and has advantages over both individual systems. Thanks!