You are reasoning as a human with an obvious bias or cultural influence. You are allowing your own knowledge of Earth events to color your conclusion.
Since when was reasoning from actual knowledge of the subject under consideration a bad thing??
Nowhere in the episode is it explicitly stated the cultures chosen were preserved in order to save them from European aggression or disease.
It was stated that they rescued cultures in danger of extinction. The causes you mention are the only phenomena that would've simultaneously put all three of the cultures referenced in danger of extinction. Particularly since one of the cultures referenced
did not exist prior to 1600, which should in and of itself conclusively mark the earliest possible date of their relocation. The point I am making is simply that the Preservers are known to have been active
in this millennium. That is unambiguous. Therefore, it is illogical to assume, as so many fans have done, that they were some ancient race that died out thousands or millions of years ago. Native American civilization in
any form only dates back maybe 12-14,000 years across most of the continent, and anatomically modern
Homo sapiens is only 40,000 years old, so the desire of some fans to see the Preservers as being millions or billions of years old is completely bizarre.
As Timewalker asked, why preserve these cultures and not the Aztecs, Inca, Maya, or any other South American cultures. Why not preserve any African cultures? European aggression and disease threatened pretty much the entire globe.
Why in the world do you assume they didn't? Once again, you're making an assumption that's contradicted by the explicit dialogue in the episode:
McCoy: "I've always wondered why there were so many humanoids scattered through the galaxy."
Spock: "So have I. Apparently the Preservers account for a number of them."
So we've known all along that the Preservers seeded multiple worlds. It stands to reason that each one is inhabited by a different culture.
Why should aliens even care about these particular cultures from becoming extinct and needing preserved? The reasons you give are valid from a human standpoint. Aliens might have an entirely different line of thought and reason for choosing whom they chose.
"They passed through the galaxy rescuing primitive cultures which were in danger of extinction." Spock's own words based on his translation of the Preserver texts. You're not arguing with me now, you're arguing with Spock.