The text box I am writing this in and use to answer questions interferes with my normal browser usage quite a bit, anyone like myself who uses any sort of extension that changes editting areas (Emacs / Vim keybindings) would appreciate the ability to just write the markdown ourselves in a plain old textarea. At the moment the box is a constant source of frustration as you can imagine.
Why don't you just disable it via a user script? I'm not really kidding here.
In the scenario you describe, you're already modifying the browser which is causing the problem in the first place, so why not write a user script to disable the WMD editor? Note that you'd lose a lot of functionality like draft saving as well...but that seems to be precisely what you're after.
For example, here's a user script that disables the hotkeys: Is there a way to disable the hotkeys?
As argued in another answer you can edit text areas with an editor instead. Then you edit in an environment that works like you want.
Text areas can be integrated with an editor of your choice via plugins such as the Firefox plugin It's All Text. With such a plugin you can effectively switch from editing in a text area to editing the same text in an editor. An example on how to use that plugin is found in an answer to Emacs mode for Stack Overflow's markdown.