Why do you think Sigma, Tokina, Tamron and Samyang were able to make those 3rd party lenses?
Ml is indeed a little bit like 3rd party lens manufacturers - they essentially help Canon because if they weren't here Canon would sell *less* cameras, it would be like Apple or MS only allowing their own applications. Canon just wants to be ahead of them to be able to put a premium on its own (L) lenses, and Canon is sure to introduce little annoyances now and then to make using 3rd party gear a bit of a hassle.
But they could of course completely block non-Canon equipment if they'd loose money - that's the point. Hacking the 1dc is such a case, they could easily change/encrypt their firmware so ml would not run on newer camera bodies - is a hacked 1dx worth having no ml on the 6d? And Canon would/could even change the 1dx production right now to further prevent any hacks - they can, because unlike rooting ios/android no user software runs on Canon os that could exploit security holes. Ml just conveniently uses a Canon mechanism to run, that could be taken away anytime with the next firmware update.
Next to that, Canon could sue the devs and refuse warranty on any camera running ml - that would diminish the userbase and bleed the project dry except for some devs profiting from hacking the first batch of 1dx.