I think it's not possible, but would like to know for sure either way.
I definitely think anyone considering installing Magic Lantern for the first time should be told if there's no way to do a complete uninstall.
I've been trying for several days now to remove all traces of the RAW video version of Magic Lantern from my 5D Mark III.
It's easy to delete the ML files from any given CF card, and straightforward to use EOScard to stop a CF card being bootable, but I can find no way to disable the bootflag in the camera.
I've searched these forums pretty thoroughly and spoken to a few people on here, but AFAIK no one knows how to disable the bootflag on the MKIII, so no one knows how to uninstall ML fully.
This thread "HOW ML START (or why it doesn't boot topic) & Restore Camera Settings"http://www.magiclantern.fm/forum/index.php?topic=2522.0
explains how ML and the bootflag works in terms of install.
It gives a method to uninstall ML:
1. Start the firmware update procedure (with battery full, no accessory, M mode...) from canon menu and wait the green text.
2. change mode on the dial and wait the white text.
3. Restart camera, clear settings and Custom Func. and format card, low level (NOTE: you will lose also your pics of course).
But that method doesn't work on the MKIII as far as I can tell, because in point (1) it never gets to the point where there's green text on a black screen.
The wiki page gives no more help, because I think it's referring to the same method:http://wiki.magiclantern.fm/faq#how_do_i_uninstall_it
a1ex suggests disabling the bootflag on a 60d on this thread http://www.magiclantern.fm/forum/index.php?topic=5594.0
"placing Canon FIR on the card"
Mikkel S. says on this thread http://www.magiclantern.fm/forum/index.php?topic=3852.0
"I put the 1.1.3 firmware from Canon (5D300113.FIR) on a blank card and turned on the camera."
but he's not sure if that really disabled the bootflag or not and it definitely doesn't for me.
I've now tried every combination of ML, ML+Canon and just canon .fir files on bootable and non-bootable cards, but none of them get me to the green text on black screen that I think is required to disable the bootflag.
I've used ML on my 5D2 (two of them) for several years, and I've been using the alpha Mk3 software for many months, without any problems.
My preffered method with the MK3 is to run the ML Alpha from the SD slot, using the CF slot to store pictures and movies.
I can leave the 5D2 ML files on all my CF cards, and this way can share CF cards between cameras. With the bootflag permanently enable in my mk3 that no longer works.
I also have an Eye-Fi card, and the ML wiki makes me think this now won't work reliably.