Yes, you're probably right. I didn't want it to include any HTML (to make it easy for anyone to contribute to course website), but perhaps there is a way to use a simple Markdown for GitHub pages.
I think jekyll[0] works really well in conjunction with github pages for exactly your use case.
Well, I use Octopress (similar to this) for my own blog. But, for the course, where I wanted all the students and other staff members to be involved, I wanted something much more simple. More specifically - nothing that would require building. Perhaps that could be just me and my preference.
This might be a good solution if people want something a bit more fancy as a course website. Thanks for sharing.