Open up wmd.js.
Look for this section:
// -------------------------------------------------------------------
// YOUR CHANGES GO HERE
//
// I've tried to localize the things you are likely to change to
// this area.
// -------------------------------------------------------------------
// The text that appears on the upper part of the dialog box when
// entering links.
var imageDialogText = "<p style='margin-top: 0px'><b>Enter the image URL.</b></p><p>You can also add a title, which will be displayed as a tool tip.</p><p>Example:<br />http://wmd-editor.com/images/cloud1.jpg \"Optional title\"</p>";
var linkDialogText = "<p style='margin-top: 0px'><b>Enter the web address.</b></p><p>You can also add a title, which will be displayed as a tool tip.</p><p>Example:<br />http://wmd-editor.com/ \"Optional title\"</p>";
// The default text that appears in the dialog input box when entering
// links.
var imageDefaultText = "http://";
var linkDefaultText = "http://";
// The location of your button images relative to the base directory.
var imageDirectory = "images/";
// Some intervals in ms. These can be adjusted to reduce the control's load.
var previewPollInterval = 500;
var pastePollInterval = 100;
// The link and title for the help button
var helpLink = "http://wmd-editor.com/";
var helpHoverTitle = "WMD website";
var helpTarget = "_blank";
var wmd_options = {"output": "Markdown"}; //ADD IT HERE
// -------------------------------------------------------------------
// END OF YOUR CHANGES
// -------------------------------------------------------------------
This will send all of your output to the database as Markdown text.
If you want to convert HTML to Markdown text for editing, because you are storing your input in HTML form, then you will need something like this:
http://milianw.de/projects/markdownify/
So when your user clicks on their 'edit' button. You run the query as you normally would, but you run the display text through Markdownify.