The current ML that runs on a 50D or 550D is basically an "application" whereas the Canon firmware is the "operating system". Fortunately this means ML installs on its own folders on your card and it does not alter the camera's internal flash memory that is dedicated to storing the Canon firmware.
So it's dirt simple to remove this version since it resides entirely on the card. Just delete the files and just to be sure, reformat the card. The easiest is to pop the card in a PC card reader and use Windows file manager to delete everything. then put the card into the camera, turn on the camera and reformat it via the menu commands. The reason you want to do this in the camera is because it also builds a couple of default folders required by the camera. Plus I've heard some card readers cause problems when formatting.
Now there are versions of ML that are specific to 5D2 that I believe are actually replacement firmware (or "operating system") as opposed to "application". I've been reluctant to install those on my 5D2 for sake of caution, and the fact the guy behind the "application" version is adding 5D2 support.
All to say I'm completely comfortable with the "application" version that runs on 50D, 550D and soon 5D2 but not so comfortable with the "firmware" versions. The rationale being that a firmware is basically the operating system for the camera and it resides on the camera's dedicated flash memory - so a bit invasive for my tastes to replace that with non-Canon code if I don't particularly need the features it has. Hope this helps clear things up for you.
All of this said, for me the focus peaking is the one thing for stills that I find useful. The auto-trigger on focus thingy doesn't really work for me - have never gotten an infocus shot with it despite my AF MA being spot on - but that was always testing with shallow DOF. But the focus peaking is awesome as long as lighting is such you can see the screen.