I don't believe there is an add-on for it, or any instructions on how to do it. However, you should be able to extend XenForo_BbCode_Parser::render($text, $extraStates) to call a Markdown parse renderer (into BB Code or straight HTML, HTML would most likely be better) and then send then call the internal render function. So...
class MarkdownEditor extends XFCP_MarkdownEditor
public function render($text, array $extraStates = array())
$text = $this->_renderMarkdown($text);
return parent::render($text, $extraStates);