The EOSM cannot currently record in mv1080 mode though it is within the capability of the camera and it seems to be a "possible" Magic Lantern feature request.
I'm wondering if there is any possible way to get mv1080 on the EOSM but I take it that has been tried before.
It wasn't tried too hard 
Looking a bit in forum history, it seems like in the very first implementations of raw video, there was a (undocumented) way to do it: http://www.magiclantern.fm/forum/index.php?topic=5860 and http://www.magiclantern.fm/forum/index.php?topic=12022
Maybe I should revisit it, but that would be a different topic.
a1ex explained that there are other ways to capture raw video. Perhaps one of these alternate methods can capture the data after it has gone through the focus pixel annihilation process?
I wouldn't really say there are "other ways" to capture raw video, there are just other possible video modes. Capturing them is the same, you just have to figure out how to get Canon firmware to put the camera in those modes. The EOSM is unique b/c Canon firmware doesn't put it into mv1080 until you start recording (H.264). So if you want to record raw video on mv1080, you have to do it while also recording H.264 at the same time (ML prevents you from doing this now a days, but it was possible in some old versions when raw video just came out). That or do some reverse engineering to figure out how to put the camera in mv1080 without starting recording. All other cameras go into the video mode you selected in the Canon menu immediately, so actually mv1080 is pretty much the "default".
Let me try to sell this feature request by stating some of the reasons I believe why the lowly EOS-M is perhaps just as important to moving Magic Lantern forward as the 5D mark III.
The camera is the least expensive of all the ML capable cameras which makes this the ideal model to experiment without being too concerned about bricking an expensive piece of photographic equipment. It is so affordable that multiple bodies can be had for less than the cost of higher end models. In fact you can get 10 EOSM bodies for the price of one 5D3--I myself have 4 bodies, yeah I'm crazy.
At first the EOSM may seem radically different from the other Canon models because it is a mirrorless but the internals are very similar to the DSLR's. The advantages include not having to lock up a mirror to get into Live View and a shorter lens flange distance so many lenses can be adapted for use on this camera.
Canon EOSM with C-mount lenses
Though the EOSM may feel like a toy compared to the DSLR's it actually has quite a rugged metal body and can stand up to the riggers of a documentary project I'm working on. I planned to use it as a spare body for a 5D3 setup but it proved capable enough as the 'A' camera. (When I was a professional still photographer back in the day I would never consider going on a job without a backup camera body.)
EOSM documentary rig
The EOSM can also be an ideal replacement for a director's viewfinder and with a PL adapter the camera can be used to look through professional cine lenses. Adding mv1080 also gives the capability of shooting much higher quality tests than with H.254 video.
EOSM with PL mount adapter
Adding mv1080 on the EOSM will also elevate this platform to the same level as the rest of the Magic Lantern capable cameras though filmmakers may want to dress it up a bit in order to be taken seriously.
EOSM Shoulder Rig with Follow Focus
There are disadvantages to the EOSM. One problem for video shooters is the short battery life though extra batteries are very affordable and it is very simple to rig up external power supplies. Another problem is that it responds slower than other cameras in still photo mode though it is just as quick as the other cameras in video mode. Speaking of still photo mode, there's that pesky shutter bug when using Magic Lantern but that's a different topic.
