Well first of all, I disagree with your assertion that top comments with contrary viewpoints might prevent groupthink. Sometimes being contrary is inherent to groupthink. And being well-written and productive doesn't mean the comment is insightful, intelligent, or informative, which one assumes would be a preferred top comment. (personally I think promoting comments that are well-written, productive and contrary just gets you a class of people who can bicker in a very civilized manner, like two English gentlemen having a polite row)
Why do we vote in directions? It would appear that according to social media, we only have one orientation in voting (vertically) and can thus only go in two directions (up and down). But this makes no sense. For one thing, the 'direction' of a comment/conversation may go many different ways... conversations do not go in a straight line. And the idea of 'elevation' in a conversation is also confusing: if anything, a conversation would be more three-dimensional than two, moving around a changing landscape.
In addition, 'up' and 'down' gives an immediate subconscious reaction where 'up' is associated with goodness (and therefore correctness) and 'down' with badness (and therefore incorrectness). I say this moral implication is the default because it makes no sense for only one direction to be correct, unless you needed to know where you were supposed to go, and your default assumption was that you should never go down. (That would be a bad presumption for airplanes, for example, as they would never land until they ran out of fuel)
So what does it mean when HNers 'vote down'? Are they agreeing with something, or disagreeing? Are we assuming they're trying to impose a nuanced influence on a particular part of a person's commentary? If it was a generic part of their comment, was it their moral or ethical stance, or their writing style, or the correctness of their comment? We have no idea; all we know is they wanted that comment to go 'down'.
A simple vote down, regardless of its supposed intent, doesn't provide any specific benefit if it comes without context. The lack of a down vote would do the opposite, however: it would force people to only be able to provide positive feedback, or no feedback at all. How does this effect group dynamics? It actually works on individual behavioral conditioning: provide positive feedback, and you get positive behavioral conditioning, and negative behavior gets weeded out automatically (because the individual wants to be rewarded, which it knows it only gets for positive behavior). This is what practically all dog-trainers and child psychologists suggest as the best method to promote positive behavior. This would have two similar effects: people would be nicer, and they would provide 'better quality' comments.
So I think 'downvoting' is a loaded and useless way to regulate comments. I think that valid alternatives would be votes for specific feedback, or if you wanted to provide a way to simply "move thread position", a button that said so specifically. These would create specific, immediate changes in the group dynamics and the interactions of the users, unlike a generic downvote button. If you're trying to prevent groupthink, give the users tools to allow them to express themselves better.