It's a great post, Dirk - and I find your continued experimentation with Jekyll / Github for course hosting exciting. There are two key questions this made me think about. They are questions about the direction of the tool, rather than anything in your post. I hope it's ok to raise them here.
(1) Who is the audience (for the post, but also for the tool)? The way it is framed is not quite technical enough for the people who might want to tinker with their course-sites (and for whom, the fact that this uses github and Jekyll is maybe enough to experiment with it) but to less technical folks it is not clear how this is better than wordpress (and I'm not sure it should be better for this particular audience).
(2) How can we support P2PU style/peer-to-peer/social learning? At least in its initial form, the only way to make Jekyll social is by embedding a discussion widget. I use Discus on my blog, but one of the projects I'm involved in at the Media Lab uses Facebook comments. I think github offers very exciting possibilities, including collaborative course development, or joint development of a core template that lots of people use and improve (with improvements flowing back into the core) but how those things would work isn't clear to me yet. If we focus on Jekyll as a way to host static content I find it less exciting.
I'd like to write more, but have to board my flight ... let me end by repeating that I am a HUGE fan of your work here and am excited to think through these things together. I think this has a lot of potential.