Mega Evolution was already established as an old, but unknown, technique in Kalos, so they didn't have to contradict anything by having it in a game set about 10-16 (rough est.) years ago. Scientifically, things can be relatively 'new' for quite a long time, especially if they're not commonly observable, which plays in to it because we've seen Mega Evolution as a resource so far limited to:
Evil Team Leaders/Admins
Champions
Elite Fours
Mega Evolution Succesors (Korrina, probably Gurkinn before her)
Lore Keepers
Rivals (Two of which had connections with a Professor and one of which had a connection with the Mega Evolution Guru)
And actually, despite the fact I find the idea stupid, removing Mega Evolution is a real possibility, regardless of how low. It can make sense from a story standpoint, by having S&M take place in the 'Original Timeline', and removing the Mega Stones and Key Stone aren't exactly a difficult task from a game design standpoint.
EDIT: Also, I don't see why you mentioned the Meta Game. If GF cared that much about it Mega Rayquaza and Mega Khangaskhan wouldn't exist and/or be nerfed.