org-ruby is much better in newer versions at coverting org documents containing
code blocks. Make sure that github/markup uses that power.
I tested org-conversion via github/markup with version 0.6.0 of org-ruby; it works.
Require org-ruby to be at least version 0.6.0.
Merge branch 'master' of git://github.com/github/markup
I try it now by following the "Contributing" instructions to the letter... :-)