Earlier quoted context omitted.
That comment was flagged by the time we saw it. 20 minutes is not nearly long enough for the community process to complete, and instantaneous moderation is impossible. Nor would it be a good thing if it were possible.
Something that seems plain to me: if overtly malicious troll comments can survive at the tops of threads for 20+ minutes, and troll-ridden threads get (reasonably!) flagged off the site, then trolls have a hecklers veto on HN.
You don't know if that comment was malicious (I don't think so), it survived long because apparently not that many people share your opinion that it should be gone (really, it only takes a few downvotes and flags to kill) and the thread got flagged off the site because for the last half year or so all controversial threads are hammered as soon as they reach the front page.
So while your logic is sound, there is no reason to panic because the assumptions don't hold.