I agree with what you are saying about the name John, though while you are associating it with something negative she is associating it with something, someone, positive. You have to tread carefully here because it clearly means a lot to her, although you also have to make your feelings clear because it could potentially be the name of your son. Maybe you could explain to her that its not a favourite name of yours, but what about having it as a middle name? Or you could even suggest similar names....I cant think of any for John atm, but like Mary is derivative of Margaret.
Hope this helps!