Two reasons come to mind, one historical and one practical:

First, the pingback implementation in WordPress was one of the more common vectors of WordPress' endless parade of security vulnerabilities. I remember years ago it was common practice to disable pingbacks (or even rip out the code) as a security precaution.

Second, pingbacks direct readers away from the site. This is good for readers and the online community as a whole, but bad for online publications which want to use comments as an "engagement" tool.

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.