Mutants/X-Men are still too important as brands to Marvel for them to actually do anything too drastic.
(In comparison the Fantastic Four simply hasn't been very popular for a while now, and I can see the cancellation could make perfect sense even without any conspiracy.)
If the film rights go unused for too long, they are reclaimed by Marvel. At which point they'll probably be retconned back or something.
They're clearly pushing Inhumans as a substitute in terms of developing new superpowered characters though. Of their optioned film rights, the X-Men/mutants are probably the least likely to return so it makes sense given there's no point trying to create breakout new characters only to be unable to use them in film.
Fox already lost the rights to Daredevil, Elektra, Kingpin et al.
When what sounds like a clusterfuck of a Fantastic Four movie bombs, I don't think they'll be so adamant about holding onto those.
Meanwhile, Sony seems to have no idea what to do with Spider-Man, and the lucrative merchandise rights have already been sold back.
And while the recent X-Men films have been good, I'm sure they'll find a way to ruin it eventually.