Am I right about any of this?
It appears that a comment which makes a point that's already widely accepted, whether true or false, tends to get more upvotes than a comment which is more controversial - again, whether true or false. The controversial yet true comments are usually more interesting and valuable. (Maybe that applies even to false controversial comments.)
Fortunately, I think most people here care more about saying what they want to say than about getting more upvotes. So I'm not saying something needs to be fixed or that I have a much better idea. Still, I think it's a reason to be cautious about taking someone's karma score very seriously. Forgive me if I'm just saying things you already know.
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.