> A good place to put the GUI for it

Tools -> Extensions -> WakabaMark

Really, this seems to be the most convenient way for me to keep the ability for markup and not annoy the users all the time or forcing them to go out of their way to disable something that's built into the site itself.
Adding more and more options to the site seems to be leading to eventual design overkill. Which brings to mind: Stylesheet selection could also be outsourced to an extension. But meh...

The main point for me here is that the markdown should not take place on the side itself in that it actually writes the <em> tags into the HTML code.

I like how Thunderbird does this (although I know the analogy is slightly flawed), it only interprets the markdown. It doesn't automatically rewrite my markdown into some HTML characters and then sends the EMail as HTML or something.