I think this is directly relevant to the idea of embracing contrarian comments.
The idea of having extra categories of voting is problematic, because it's always easy to suggest, but only worthwhile if people will often want to distinguish them, and distinguishing them will be useful. So I think normally it's a well-meaning but doomed suggestion, and better to stick to just one.
However, whether or not it would be a good idea to actually imlpement, I think separating "interested" and "agree" is a good way of expressing what happens to contrarian comments. I don't have first-hand experience, but based on what I usually see happening at message boards, I suspect a common case is something like:
Someone posts a contrarian comment. Because they are not already a community stalwart, they also compose the comment in a way which is low-status within the community (eg. bits of bad reasoning, waffle, embedded in other assumptions which disagree with the community).
Thus, people choose between "there's something interesting here" and "In general, this comment doesn't support the norms we want this community to represent." The latter usually wins except when the commenter happens to be popular or very articulate.
The interesting/agree distinction would be relevant in cases like this, for instance:
There's a possibly similar distinction between stackoverflow and stackoverflow meta, because negative votes affect user rank on overflow but not meta. On stack overflow, voting generally refers to perceived quality. On meta, it normally means agreement.
I'm not sure I'd advocate this as a good idea, but it seemed an interesting possibility given the problem proposed. FWIW, if it were implemented, it'd want a lot of scrutiny and brainstorming, but my first reaction would be to leave the voting as supposedly meaning "interesting", and usually sort by that, but add a secondary vote meaning "agree" or "disagree" or similar terms that can add a nuance to it.
Edit: Come to think of it, a similar effect is acheived by a social convention of people upvoting the comment, but also upvoting a reply that says "this part good, this part bad". If that happens, it should fulfil the same niche, but I don't know if it is happening enough.
I'm worried that LW doesn't have enough good contrarians and skeptics, people who disagree with us or like to find fault in every idea they see, but do so in a way that is often right and can change our minds when they are. I fear that when contrarians/skeptics join us but aren't "good enough", we tend to drive them away instead of improving them.
For example, I know a couple of people who occasionally had interesting ideas that were contrary to the local LW consensus, but were (or appeared to be) too confident in their ideas, both good and bad. Both people ended up being repeatedly downvoted and left our community a few months after they arrived. This must have happened more often than I have noticed (partly evidenced by the large number of comments/posts now marked as written by [deleted], sometimes with whole threads written entirely by deleted accounts). I feel that this is a waste that we should try to prevent (or at least think about how we might). So here are some ideas: