Agreed. The numbering, for me, is a good sign of which comments to keep an eye on while scanning the page, rather than get lost in text.
Maybe making the default text color slightly more grayish and the "a bit better than orange dot" have #000 text, and for the exceptionally upvoted posts also make the "pg 26 minutes ago | link | parent | flag" header bold.
These things aren't perfect measures, but I find them useful.
By reading every post you'll certainly find the "diamond in the rough", posts that don't get the recognition they deserve. But you'll also have to trudge through loads of posts of little merit. Given that there is an infinite amount of information on the internet, those 2 minutes can probably be better spent on wikipedia or reading the top post in a different HN thread.
Additionally: HN isn't just about opinion, it is also for a large part about fact. And insightful facts almost always rise to the top. On the bottom of threads you often find things that are wrong or subtly wrong.
Judging by the numbers may very well be the most efficient and reliable way to get to insightful content.
And of course these dots will help you locate higher rated comments that get pushed to the bottom (perhaps because they replied to a low rated comment).
BillSwift your comment has all of the sniping dogma that you attribute to Herd Followers.
Have you tried to think of a more generous reason that people might look at the scores? perhaps people (like me) do a first pass to understand the herd reaction, and then do a second pass to delve into the specifics.
Simply saying score readers are herd following cretins is insulting and wrong.