Wanda had innate powers, just not very strong, the mind stone enhanced what was already there. Wanda using the power of the mind stone she possesses could activate latent powers in others (see Monica Rambeau). That means no origin stories have to change - mutants had powers all along, they're just activated and controllable now.

Of all my predictions I think this one is actually not very likely considering no X-Men movie or series has been announced yet, so the dawn of MCU mutants may not be as imminent as fans want.