While I would never support it, the main way to improve online discussion is by removing anonymity. Allow me to go back a couple decades and point to John Gabriel's Greater Internet Fuckwad Theory. People with a reasonable expectation of anonymity turn into complete assholes. The common solution to this is by linking accounts to a real identity in some way, such that online actions have negative consequences to the person taking them. Google famously tried this by forcing people to use their real name on accounts. And it was a privacy nightmare. Ultimately though, it's the only functional solution. If anti-social actions do not have negative social consequences, then there is no disincentive for people to not take those actions and people can just keep spinning up new accounts and taking those same anti-social actions. This can also be automated, resulting in the bot farms which troll and brigade online forums. On the privacy nightmare side of the coin, it means it's much easier to target people for legitimate, though unpopular, opinions. There are some "in the middle" options, which can make the cost to creating accounts somewhat higher and slower; but, which don't expose peoples' real identities in quite the same way. But, every system has it's pros and cons. And the linking of identities to accounts

Voting systems and the like will always be a kludge, which is easy to work around. Any attempt to predicate the voting on trusting users to "do the right thing" is doomed to fail. People suck, they will do what they want and ignore the rules when they feel they are justified in doing so. Or, some people will do it just to be dicks. At the same time, it also promotes herding and bubbles. If everyone in a community chooses to downvote puppies and upvote cats, eventually the puppy people will be drown out and forced to go off and found their own community which does the opposite. And those communities, both now stuck in a bias reinforcing echo chamber, will continue to drift further apart and possibly radicalize against each other. This isn't even limited to online discussions. People often choose their meat-space friends based on similar beliefs, which leads to people living in bubbles which may not be representative to a wider world.

Despite the limitations of the kludge, I do think voting systems are the best we're going to get. I'd agree with @grue that the Slashdot system had a lot of merit. Allowing the community to both vote on articles/comments and then later have those votes voted on by a random selection of users, seems like a reasonable way to try to enforce some of the "good faith" voting you're looking for. Though, even that will likely get gamed and lead to herding. It's also a lot more cumbersome and relies on the user community taking on a greater role in maintaining the community. But, as I have implied, I don't think there is a "good" solution, only a lot of "less bad" ones.