You can't reference files outside the webroot (your Sites folder, in this case); that would potentially allow access to any file on your machine.
If you want to solve this without moving your repo, you can symlink your GitHub dir into your Sites folder. On OS X, Apache should follow symlinks by default; if not, you can place a .htaccess file with Options +FollowSymlinks
in the Sites folder to turn it on. (You can find the docs on Apache's Options
directive here).