If they truly think they're right they might just downmod using both methods. I assume a lot of people who think a comment is wrong, might also think it is stupid.
That's a great point, but the nice thing is that you can actually detect that programatically. If a user always votes both up or down, the software can remind them of how they are supposed to vote.
Or the software can just ignore people that vote both up or both down. The more interesting and 'telling' votes are those who agree but vote down, or disagree but vote up. Of course, it would behoove pg not to tell the secret, otherwise people would simply game the voting.
Overengineer much? The current system works.
The best way to disagree is already possible: reply to a comment by stating your opinion. Off course that can have negative effects on signal/noise ratio (or not?).
That is a frequent request for sites that have votes. It would be an interesting experiment to try it out on hn or some similar system to see how it handles.