Let's take Hacker News as a case-study. The open registration system without email verification or any sort of verification allows users to comment and act without retribution or fear of being called out. While I support strong security and encryption, generally being anonymous on the internet promotes negative behavior.
Anonymity on the internet causes people to act inappropriately, troll, comment offensively, conduct fraud and illegal activities.
Interesting, because I think your example is even more effective as a counter-example to your point. As you noted, Hacker News is pretty anonymous, and without verification. Yet, compare the comments here, with Facebook comments on pretty much any news site. Or maybe any other site with Facebook comments. There is no comparison -- Hacker News, with all its anonymity, is much more civil, collegiate, and productive.
The lack of intelligent, earnest discourse online is much more complex than anonymity or the lack of it.