Compared to Reddit, HN has a way, way smaller number of instances of "downvote to disagree". You can't prevent it entirely because sometimes it is the right behaviour (such as someone spouting crap on vaccines causing autism, for example...), and sometimes there's an opinion people feel too strongly not to downvote but not strongly enough to reply instead.
But the amount of times I've seen controversial opinions rise to the top just because they're thorough and elaborate has been really fantastic, and I make sure to upvote things I disagree on myself. On reddit, the top comment tends to be a one-liner pun -- and again, it feels wrong to me to upvote things I disagree with on Reddit, so I don't do it and it just makes the whole situation worse.
I think HN should make voting more structured. I'm not sure why my karma should suffer if I don't have a popular opinion. Such example is low-carb diets. I always get downvoted, because most people are hooked up on carbs. Why should my karma reflect that? A niche like hackers penalizing niches is not very karmic!
But the amount of times I've seen controversial opinions rise to the top just because they're thorough and elaborate has been really fantastic, and I make sure to upvote things I disagree on myself. On reddit, the top comment tends to be a one-liner pun -- and again, it feels wrong to me to upvote things I disagree with on Reddit, so I don't do it and it just makes the whole situation worse.