I just released Jekyll 0.5.0 which contains a huge overhaul that allows you to specify options in a _config.yml file. GitHub Pages will honor most of these settings, so if you want to have your Page rendered with RDiscount instead of Maruku, just put this in your config file:

markdown: rdiscount

And if you’d prefer to use a different permalink style, you can set that too:

permalink: pretty

This release also contains tons of bugfixes. More info on GitHub Pages at http://pages.github.com and be sure to peruse the Jekyll Readme