Oh, I get it. Those plugins are "compile-time" -- so they happen during the HTML generation process, before going up to github -- all github ever sees is static HTML and CSS files.
I played with Jekyll on GitHub several months ago, but as I recall, you commit your source files to the repo, and the GitHub would run Jekyll to compile them to HTML. (And send you an annoying message every time that it was successful...)
Could you have this as a two stage process? Make changes to files, push to my repo, repo hook runs jeckyll, commits new static assets, and pushes to github? This does require using a central server other than github I guess, though...