I agree. I would rather keep rmarkdown separate and tools designed in R to handle the parsing/conversion part. That way we can capitalize on Rstudio without going back and forth while writing the post. My feeling is we can do so easily if we can somehow leverage rstudio as the daemon and / or some package designed in R (knitr?) to export ‘.Rmd’ files stored in _rmarkdown folder and converted to html/ md and posted in _post folder. But I am not sure . Here is a blogpost where someone has converted Rmd to md.
http://brooksandrew.github.io/simpleblog/articles/blogging-with-r-markdown-and-jekyll-using-knitr/
Since , I am just starting with R. I don’t know how to adapt this effectively to a script which we can use outside Rstudio. With this we may not get all the features, for show/ hiding code etc… But may be we can gradually adapt it