This all seems to me like clever storytelling and writing that basically explains what she has been all along. I expect her mutant status to be reversed in the books as well probably in SWORD where we have seen Magneto refer to her in a sorrowful way. I think things are going to come to a head between the X-Men and Wanda with the kree/skrulls and she will be back to being a mutant when it’s all said and done...