This entire experience has left me with a bad taste in my mouth about Jeff Atwood -- I sure hope he doesn't set his sights on something useful that I've created for the world. You can make whatever argument you like about Gruber not "paying enough attention" to his creation, but Markdown doesn't really need to be "fixed" or "standardized". I look forward to the, undoubtedly, dozens of vendor-specific extensions that will be necessary in the final product and we'll end up right back at square one.
Really, really presumptuous and poor judgment. Invent your own stuff and let it stand on its merits rather than trading on Markdown's well-established name by force.