I think it's the same here. People can have opinions, but once says Microsoft is great and open source sucks or something like that, you're already past the point of no return, it's inevitable the thread or sub-thread will devolve into a flame war.
Certain threads are this way starting from the original topic. Like the threads, amidst the recent threads of falling programmer salaries (or perhaps mentions of the historically high unemployment rates) of the desire of the SV barons to raise the H1B cap. This again is guaranteed to degenerate into a flame war.
My unscientific study of HN is that someone can get a lot of karma for saying why they think Obama is good or bad or the like. A post on that guarantees a dozen upvotes. Someone making a cogent comment on how a company should limit the scope of what parts of C++ they use is not going to get as much karma.
I have been on BBSs since the 1980s. The real problem of a forum is this. It has a handful of very sharp, interesting people who like communicating with each other and who write good posts. Then you get some blabbermouths who post and post and post and fill the boards up with junk. Then the good people leave. The good people leaving is the problem.
I don't think flames are the only thing to be concerned with. Blabbermouths who have nothing to say kill boards as well. Have flamewars killed the Linux kernel mailing list? Just as long as things are kept under control. The NetBSD/OpenBSD flamewar got out of control.
Slashdot is a board that was good and had its founders leave and is all corporate and user-view baiting now. What are its topics right now? "Google's Nexus Q Successor Hits the FCC". Who cares? "John McAfee's Belize Home Burns To Ground". I can survive a few weeks without an update on McAfee. "NetBSD 6.1 Has Shipped". Something only the dwindling remainder of NetBSD fanbois care about.
Certain topics and upvoted threads, once existing, are going to turn into a flamewar no matter what. It has to be rooted out early on for anything to be effective.