I think that a protocol or standard is part of the solution, but it really needs a service (or any number of them) to track the whole graph of replies.
The kind of aggressive court interference talked about in the article, will (or at least should) be the catalyst to make that happen.
Anonymous comments really ought to be hosted anonymously and in a distributed fashion, preventing them from being taken down or "used against you." The "fire in a crowded theater" supposed exception, is simply not relevant wrt internet comments.
