Patriarchy is "completely unnatural" you say, but so is drinking milk, and that sure got fixed in a lot of populations pretty well. What does it even mean for something to be "unnatural" if we do it in a widespread way for thousands of years?
You also just pulled 200,000 years out of a hat. I mean, a lot of people like that hat--it's not just you. But is there anything special about the scope of genetic changes that could happen in 200,000 years but not 9,000 years? Not really! You can definitely do more in 200,000 years than 9,000, but you can do even more in 6,000,000 or 25,000,000!
Chimps and gorillas are patriarchal. Baboons are patriarchally matriarchal with Andrew Tate style males in less stable hierarchies (as a general rule, but this seems somewhat culturally malleable!). Among hominids, Homo sapiens has one of the more equal body sizes between males and females...but it's still rather unequal. This is all consistent with non-"patriarchy" being "completely unnatural" (on a different timescale).
And if you throw in bonobos, and think hard about baboons (and different types of baboons), not to mention gibbons and orangutans with their very different social structure, then you start to wonder whether our whole lineage hasn't had the flexibility to embrace patriarchy or matriarchy (with varying degrees of hierarchy, monogamy, and violence) for tens of millions of years.
If you're going to argue against Amanda's points, you need to do a lot better than this. I think one could argue against a few of her points (if nobody else has, I will...I still haven't read all the comments). But you're just telling an alternative mythology to Amanda's. We do know enough to rule out some of the most extreme albeit widely told older myths about human history. For instance, "nasty, brutish, and short-lived patriarchy, universally, back to our common ancestor with chimps", is known to be wrong because we have too many counterexamples. However, we don't know anywhere near enough to confidently support almost anything you said. The idea that this is settled science is absolutely a myth--and I'm perfectly happy to go as deep as you care into the primary research to settle the matter.