Exactly. Plenty of high-profile blogs that are powered by wordpress also use disqus. Using disqus != using a site generator (jekyll), and using jekyll != using disqus.
The same could be said for those of us who use posterous to power our blogs. I think what the author of the article really wanted is to suggest a free/open commenting platform similar to disqus. I wonder how long until we see a "Comment.js" type post now? Could be cool.
It's not Jekyll et al. that are harmful to FOSS. The author talks about Disqus being a closed system, which is true.
However, assuming that I'm using Disqus just because I'm running a blog on Jekyll isn't a fair claim.