The quote above is a case in point: you say that the "strongest argument" for downvoting rude comments is that it "reflects poorly on" commenters.

I apologize if I was unclear: upvotes and downvotes exist to signal to two different groups: the authors of comments, and the readers of comments. To the first group they have pedagogical value ("ok, I should be posting X and should refrain from posting Y") and to the second group they have predictive value ("hmm, karma too low? I don't think I'll waste my time").

And so my argument is that if someone posts statement Z and doesn't realize that statement Z is rude, then a downvote (preferably coupled with a polite "try being less rude" comment) is the best thing for them pedagogically, since it helps them improve their ability to articulate themself. If they know they're being rude but think it helps make their point, that's one thing- but if it's from ignorance, even ignorance of social customs, then that's something we generally try to fix around here.

And, in case you're wondering, this is the sort of thing that happens to everyone. If one of EY's comments approaches the issue the wrong way, it will get voted down.

I see no reason for thinking that a community of people devoted to refining the art of human rationality should assume the task of punishing others for saying things that would reflect poorly on them as social creatures.

Rational agents should WIN. Winning often involves social interaction (especially if your goal is to persuade others).

I also note (again) that there is sometimes a tension between doing what is socially appropriate and what is epistemically appropriate.

This looks like a false dilemma. It's not "do I point out their hypocrisy or not?"- there are two separate questions, "do I raise this issue?" and "how do I raise it?". You seem to be under the impression that the only way to raise this issue is rudely, and it's better to be rude than not raise the issue. I strongly disagree; there are very many ways you could approach the issue with a little patience and get much farther than you did. For example, you could say something like "I'm curious about your justification for eating meat; would you mind telling me it?" or "Is vegetarianism an issue that's come up here before? There seems to be a lot about moral reasoning and that seems as appropriate a question as any."

Tact is a rather valuable skill, both at convincing others of their errors and leaving yourself in a social position where you can admit your errors. Both are valuable tools when it comes to refining human rationality.