Interesting idea, but I think most mutations that would so severely change how a woman responds to hormones would also be debilitating to the point that she wouldn't be able to have children.
But that makes me wonder, whatever mechanism antibiotics use to lessen the effectiveness, couldn't a small mutation use the same mechanism?
Related to the current discussion, women would quickly realize that their menstrual cycle is not lining up with the week of non-hormone pills.