Limit the number of times one person can post in the same thread to once (or maybe twice), either from the top node or a sub-node. Example:
PersonA says, "blah blah blah..."
PersonB says, "You're an idiot because blah blah blah..."
PersonA is locked out from replying to PersonB.
This will do 7 things:
1. It will eliminate argument strings between 2 people.
2. It will remove the incentive to flame because your flame can't turn into an argument.
3. It will encourage people to think through what they have to say, anticipate counter-arguments, and address them in their original comment (or with an update in the 2 hour edit window).
4. It will foster a greater sense of community by encouraging people to stick up for each other. (PersonA made a good comment, PersonB trolled, PersonA can't reply, so I will.) PersonB will get the message much better when confronted by the community instead of PersonA. (Of course, if no one sticks up for PersonA, then maybe they really were wrong.)
5. It will encourage 2 people to take their legitimate discussion (of little interest to others) off-line.
6. It will reduce the length and indentation of threads making them easier to read.
7. It will encourage everyone to slow down and think a little. Those who don't will stick out (not in a good way). Trolls will get more satisfaction somewhere else.
(This is already working by accident. I have gotten so busy that I only visit hn in short bursts. Often, when someone challenges me, I don't reply because I have left and returned much later. But others have replied for me. The resulting thread is invariably better than if I had replied myself.)