Admittedly, the reason why I think MJ might've been retconned into meeting Peter for the first time is because of the way they set it up (Aunt May mentioning Anna Watson's niece) is similar to how MJ was built up before her "Face it, Tiger..." iconic intro. So, I think a lot of us (including myself) assumed they're doing their own take on that intro.
Not to mention other inconsistencies, like Grady's redesign and no mention of Doc Connors's Lizard episode, kind of doesn't make it impossible. Again, better to wait for the next special, but I don't blame people for thinking that way.