I separated this out because it seems, well, like a separate argument.
Second, even if morality was irrefutably demonstrated to be natural
Who said the argument was about whether morality might be natural? The argument is about whether or not it's
rational. The idea that we have moral instincts that contribute to survival has never been under dispute as a possibility, and I'm not sure where you got the idea that it was.
To the contrary, you agreed earlier that it's impossible to prove any kind of objective morality through science. At most, we might be able to trace certain impulses to a related survival benefit. But that still wouldn't tell us anything about whether or not they were rational.
believers would simply adapt like they have with evolution and other discoveries that have proven their books incorrect.
1. The narrative of religion slowly retreating in the face of scientific evidence is simplistic at best and fictional at worst. Catholics contributed to the theory of evolution, and the Church (which is by no means speedy about its formal declarations) formally declared evolution as compatible with its beliefs way back in the 1950s. Famous Christian writers like G.K. Chesterton dismissed the idea that they were in conflict even earlier than that. The idea that it has "proven their books incorrect" doesn't fly.
2. Just what do you think atheism has done over time, comparatively? In the early 20th century skeptics used science to try to argue for eugenics, and the inferiority of races. And then something happened in WWII that made this view seem considerably less sophisticated. And this is still modern history! So if you have disdain for any belief which has "adapted" over time to the prevailing wisdom of the time period, you won't find any refuge in atheism, which has proved just as susceptible to the popular winds and the abuse of fanatics as any religion.
Moreso, actually, because its very nature is far more malleable than religion, which is based in more rigid principles. That's supposed to be one of the things atheists dislike about it. So which is it? Is it too rigid, or too susceptible to popular opinion? Can't be both.
3. While it's certainly true that the ancient church mistook its theological import for scientific knowledge, the opposite is happening today. We see it clearly in the many futile attempts atheists engage in to try to reverse-engineer Judeo-Christian ethics from their materialist worldview. Just as believers once mistook religious authority for scientific authority, atheists now mistakenly think they can apply scientific rigor to non-scientific areas.