You can convert R Markdown files to RTF files using the rtf_document output mode.
Pandoc has limited support for RTF. If you want to create custom RTF output (e.g. using the RTF2 package) then you can effectively bypass the rendering process with the raw_output function in the knitr package. See test-rtf.Rmd for an example. Note: this process currently requires development versions of the rmarkdown and knitr pacakges.
