I think the rationale for the policy is something like "if we didn't encourage this, we'd get a lot of low-quality comments that boil down to 'I disagree'".
I think that's bad reasoning. Disagreeing without saying why should be banned, but disagreeing why explaining why be useful. If the point of upvoting/downvoting is make the more interesting and useful comments bubble up to the top, having comments sink to the bottom because people disagree is clearly counterproductive.