While I can't speak for zedshaw, I think the problem with HN is that while it, as you say, shuns and bans anyone who speaks in an aggressive tone or who directly vituperates others, it also allows (and often supports, with upvotes) one to completely slander someone as long as they do it in a calm and reasonable tone.
If that is an example of the "slander" Zed speaks of, his response is way overboard. It has that "more hacker than thou" tone that I find annoying in anyone (and most annoying when I catch myself using it, which is often), but I can't imagine anyone would consider it slanderous. And, it is by a no-name account, which, I suspect, makes everyone somewhat less likely to pay it any mind. The idea that something like that constitutes a years-long campaign of defamation against Zed is worryingly like paranoia.
From what I can tell, I do believe that Zed Shaw has experienced abuse from a larger community over a few years, I think starting with members of the Ruby community. Some might say that Zed fans the flames of controversy by reciprocating with insults.
Perhaps he sounds paranoid because he has nobody concrete to point a finger at, which is part of the nature of being famous on the internet.
I spent a little time browsing Zed's comment history (after seeing his reply to the comment you linked). It does seem to be representative of the kind of comment Zed calls "slanderous", at least in the past year or so. Perhaps there's something else, or perhaps there are comments that Zed did not respond to, that are actually problematic in some way. But, what I see is a polite but somewhat negative review of one of Zed's books. If that is "slander", then I have slandered Steve Jobs so many times it's not funny.
We don't remove the comment scores actually :) For the first 10 days of a comment's life, HN's API always returns 0: so we index 0. After 10 days, comment scores are visible and should be updated in the index.
As an example, specifically regarding anonymous accounts and zedshaw: https://news.ycombinator.com/item?id=9276436