I did a quick search and couldn't find any topics on this although I'm sure I'm not the first person to have tried this. If this has already been posted, sorry about that, that's an embarrassing first post. So I recently bought a 50D and a 128gb CF card to go with it, it's been so long since I last installed Magic Lantern that I forgot that you could only perform a first time install from a <32gb card. Rather than go out and buy a smaller CF card that I would never use again I decided to try a work around which, surprisingly, worked.
This is how I performed a first time install of Magic Lantern on a 50D from a 128gb 1050x CF card:
All you have to do is completely wipe the card and then create a primary partition for it which is smaller than 32gb. Then you can install magic lantern on the camera as you would with a smaller card. Now you can take your CF card and reformat it so that it allocates all of it's memory to the partition, use EOScard to make it bootable and put it back into the camera.
You can wipe the card and create the partition in the windows diskpart utility, here's how:
Type diskpart into a command prompt window
The diskpart window will open, in this window type "list disk"
All of your disks will be listed, find your card and note down the disk number.
Type "select disk n" where n is the number of your card
Type list volume
All of your volumes will be listed, find your card's volume and note down the number.
Type "select volume n" where n is the number of your card's volume
Type "clean all" and wait. wait a long time. Go watch the extended LOTR Trilogy. Then go watch the hobbit films. Then write Peter Hackson an angry letter. Then wait some more.
Then type "create partition primary"
This is the mildly tricky part, you need to figure out how much you want to shrink your card by in megabytes. Just take the size of your card, subtract 16 from it, and then multiply what you're left with by 1024. Write down this number.
Now type "shrink desired = n" where n is whatever number you calculated earlier.
Now type " format fs=fat32 label="Magic Lantern" "
When you have performed the first install, you can repeat the above steps (without shrinking the drive this time though) to get your original card size back. I think performing a low level format in camera would also work but I haven't tried.
This shouldn't be at all dangerous for your card or your camera, but I can't take any responsibility if you ruin either whilst trying this. Good luck.