There's also the fact that in the comics, the X-Men were never a governmental entity (one of the things that caused them problems after M-Day). The first group of "government mutants" in Marvel were the former members of the Brotherhood of Mutants, pressed into service as Freedom Force back in the late '80s. That worked out about as well as one might expect, given that the team included Mystique, Avalanche, and Pyro...
In the 616 timeline, in fact, by the time Xavier and Lensherr were willing to "come out" as mutants, Erik had already become a mutant separatist (not surprising, given his backstory in Germany and Czechoslavakia). Mags didn't become an X-Man until, IIRC, sometime in the '90s, and that only briefly (Charles had left the planet to be Lilandra's prince consort, and asked Erik to fill in as the New Mutants' teacher); as I mentioned before, Mystique was never an X-Man, although she did stop working against them, at least for a time, after M-Day; Hank McCoy didn't experiment on himself until the late '60s, during the team's first breakup, and in fact during their first published adventure in 1963 he looked human (short, broad, and with incredibly long toes, but still human); Banshee didn't join the team until the Krakoa incident in the early '70s; Pixie (Angel, as they apparently call her in here) wasn't even born until the 1990s... there are almost certainly other discrepancies in the tales that I'll pick up on after I see the movie.
So no, there is no chance that this is going to evolve into the standard Marvel timeline. However, it might turn out to figure into the background for the timeline of the Avengers movies (Iron Man, Iron Man 2, Captain America, the last Hulk movie, Thor, and next year's Avengers movie), which Marvel has officially labeled Earth-199999. 
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Sodium is a metal that reacts explosively when exposed to water. Chlorine is a gas that'll kill you dead in moments. Together they make my fries taste good.