repdata-22 - Totally untested - but I recently stumbled upon GitBook - http://www.gitbook.io/ - which merges Markdown and Github and seems to be suited for both longish and 'living' documents, if you come up with your own workflow for transforming 'living' .Rmd files into plain Markdown files (which should not be a problem).
Just curious: does Emacs also 'inject' the output of the R code into the document like knitr does or does it just highlight the code?