I agree. They are also site-wide links, which have been discounted since about 2005.
The issue that I have with the article is that James claims that Penguin update intentionally penalized sites that offer free WordPress themes. I think there are several much more logical explanations for his problems. It appears that the author links may be creating their own Negative SEO attack or at least are setting up a lot of poor quality links. If the WPMU.org problems are due to author links, I suspect that it is due to a bug in the Penguin algorithm and will be corrected. It looks like most of the updates going forward in the near future will be Penguin updates.
"Democracy is two wolves and a lamb voting on what to have for lunch. Liberty is a well-armed lamb contesting the vote." -- Benjamin Franklin