"Cool, now there're two ways for me to punish someone I don't like." The flaw, if you want to call it that, with this suggestion is that it is a mechanism based on the idea that people are decent, reasonable, and well-informed. Which is not a bad thing, but it is not well suited to fixing a problem caused be people behaving indecently, unreasonably, and/or with little experience being "Good HN Citizens."
How the votes get turned into "punishment" will have to be tested and tweaked. I think it is worth a try, because it sets the expectation for what your votes mean be the nature of the button that you are about to press.
You seem to be thinking that this is largely trollish behavior. I suspect, however, that most of it comes from ignorance of the expectations of the community. I'm not sure there is a fix for the trolls. But for noobs that watch reality tv shows and want to come here and be the acerbic judge I think we can stop it by keeping the behavioral expectations in the forefront.
The flaw with the idea isn't what you say. I think it's important to expect decent, reasonable behavior. The flaw is, 'ok, we have two buttons. Now what?'
I would start with having the quality score 'float' the article and pretty much ignore the agree/disagree score in karma metrics. But I would probably keep that a secret.
True, unfortunately. But the flipside of having more people on the site is that there is no longer any need to ensure that everyone's comments become public on every story. You can afford to be choosier about what actually shows up, you just have to come up with a proper filtering mechanism. I think karma can be adequate, there just needs to be a more effective system of distributing and using it than what HN uses currently.
The obvious fix for that is to have slashdot style moderation where you have a single vote to assign to one of many categories: offtopic, flame bait, funny. Insightful, etc.