I'm very sorry it has come this far. It's easy to forget we have a tendency to make remarks about people online that we would never bring up in a personal conversation. I'm not excluding myself here, I too feel I'm sometimes harsher online than offline - and it sadly also happened in the Dave Winer thread yesterday. People can come across in a certain way through their writing that we would never attribute to them if…
I think part of this is just the dynamics of community-moderated comments. In my experience, the way to get upvotes in any such forum (not just HN) is to express an opinion in the strongest terms you possibly can. "X is dead" gets upvotes. "X has some challenges to overcome, and it might" doesn't. People like and respond to simple, clear arguments that don't admit weakness or uncertainty.
This dynamic then feeds on itself, as the people who are the best at forcefully stating their opinions become top commenters, crowding out more cautious voices and providing a bad role model that the next generation of would-be top commenters follows.
How do you fix this? It's poisoned so many great communities I've belonged to, so I wish I knew. But I don't.
EDIT: I have seen one mechanism that helps mitigate this: hide the users' actual karma scores.
Karma is a scoring mechanism. That turns forums that use it into a video game (of the type very well parodied by http://www.forumwarz.com/about). Participants compete with each other to see who can get the highest score. Hiding the actual numbers from users takes some of the fun out of this, which cuts down on trolling.
Slashdot used to show your exact karma score, and they had these exact same problems. Eventually they switched to just a text label ("Excellent", say, for high-karma users) that indicated your general karmic position, and the comments got a lot better very fast. Nobody's going to put as much time in to go from "Excellent" to "Excellent" as they might to go from, say, 2,500 to 5,000.