The fiction piece in this week's New Yorker deals with some of the same themes as Eliezer's "Three Worlds Collide"; viz., the clash of value systems (and the difficulty of seeing those with a different value system as rational), and the idea of humanity developing in ways that seem bizarre/grotesque/evil to us.
The scenario in which now-like humans, and future humans, find each other's morals mutually repulsive, is interesting. But we have millennia of experience resolving conflicts.
But I think that some attention should also be given to scenarios in which both the now-like humans and the future humans agree that the future humans are morally superior to the old-style humans. That seems more likely, and may be more difficult to resolve, as we have no experience with such problems.
Eh? Have you read different history books than the ones I read? We have about 50-ish years experience of resolving conflicts with seriously differing worldviews by being nice. And largely because we won so outright we could afford to be magnanimous.