I see that some of the Godzilla toys are starting to appear in shops; here's Godzilla's (and MUTO's) origin according to the back of one of the packages, spoilers obviously:
http://i.imgur.com/lr9dwW2.jpg
Hmm... that implies that the events of the original movie didn't happen, but that the backstory of the original is still largely intact. Of course, that's just a toy-package summary; there might still be room in the actual film to accommodate the '54 Tokyo attack, even if it's left implicit.