Today on the Yahoo DITA group, Jarno Elovirta announced the release of a markdown DITA-OT plugin. The plug-in adds support for consuming and producing Markdown with DITA-OT. See https://github.com/jelovirt/dita-ot-markdown for more information.for more information.
I have not installed or tried the plugin yet. According the remarks on the plugin's GitHub page, it requires DITA-OT 2.1. When I went to the DITA-OT GitHub site, the "develop" branch was the only one that met the 2.1 requirement. So, it looks like you would need to clone the "develop" branch and build it with ant by following the instructions on that page.