It almost sounds as if the concept was supposed to be that Ayla was so brilliant and so far ahead of her time that her own genius was her downfall, because her contemporaries weren't prepared to handle the implications of her advanced ideas. So not exactly a tragic hero, but more of an ice age Galileo.

I suspect a twist like that would have been hard to pull off after six books, even if the author had been firing on all cylinders. Maybe if you covered the story of the accidental birth of patriarchy in one book it could work. But after such a long time (both in page count and in years) of readers getting invested in these characters and their society, it seems maybe too late to pull the rug out from under them and expect the reaction be anything but a giant WTF?