I think whether or not someone is allowed to comment anon is really only going to affect the number of comments a writer gets. If someone doesn't want to put their name on a comment, if they don't have the option to do it anon, they just won't comment (and there can be all sorts of reasons to post as anon that have nothing to do with being rude: for instance, maybe they have one LJ account where their identity is obvious to anyone who knows them [perhaps they use it for personal reasons, professional writing, school related activities, political commentary, specific interest groups, etc...anything not fandom] and they don't want those people to know they read/comment on fanfic).

So the writer will receive fewer comments, ultimately. While allowing anon postings might upset the writer/other readers (if the anon comments are occasionally rude), not allowing them only hurts the writer (there are plenty examples are very wonderful, thoughtful anon comments). As someone who reads and doesn't write, it takes a lot of time and effort to write a thoughtful comment. If I didn't want to attach my username to it, I just wouldn't comment.

On a personal note/just as an aside: I have never commented as anon unless a posting specifically asks for that, but I do find IP address tracking really anti-privacy. For that reason, I don't track IP addresses on my journal. It's strange to me that in fandom, where so many people are really concerned with their privacy and keeping the real identity cloaked, there's such resistance to anon posting, commenting, and almost everyone whose journal I've been on tracks IP addresses. Seems like a bit of a contradiction. *shrugs*