The question is this: What happens when you ignore someone, so you don't have to see their posts, but they keep commenting on the posts of others that you follow, or on your posts? That question needs answering. I don't think its a good idea to hide all of the comments from someone you ignore, because you might lose part of an otherwise good conversation. But what is the best way to deal with it? We haven't had to cross that bridge, because there aren't any abusive users on the site (yet). But I think its a good topic to think about so that we can be prepared not if, but when, it comes up. Because as you point out, when a site becomes popular, destructive users inevitably follow. Its a good crowd source question. How should Hubski deal with a hypothetical abusive, or otherwise destructive user, bearing in mind the user-centric philosophy of the site (i.e. keeping any kind of moderator/curator as an absolute last resort)?
I think this situation is alike to that of a bully in school. How do you stop someone like that? You can (a) confront the person, but I think that would, most likely, escalate into a flame war and all the horizon of civility and politeness would be crossed much faster than any of us would like to; or (b) you can ignore the person. However, that strategy also has its problems. It might stop the bully, but it also might give him confidence to pursue his abusive behavior without consequence.
Definitely just not responding to negative comments is the best--but also the hardest--thing to do. I know that a PM service is in the works. Maybe by default ignored users shouldn't be able to send you a PM. Just spitballin'. At least that way it would prevent spam to some degree.