This entanglement is unavoidable as long as there's only one score per comment, given the interface and established practice, at HN and similar sites.
It might work to have a second axis/score that's specifically agree/disagree. (This could take the form of left-agree and right-disagree arrows, perhaps on the right of the comment-meta-line.) Then a comment could be be wildly agreed-with without offering a karmic windfall to repetitions of obvious popular sentiments, or wildly disagreed-with without the current undercurrents of censorship (sinking/fading-out) and karmic punishment via disagreement-downvotes.
Personally, I would expect to find the comments with both net upvotes (valuable) and rightvotes (disagreement) to be most interesting -- because they capture challenging minority viewpoints, but well-presented.