These SF depictions are often familiar or stereotype personalities, ideological factions, and issues of contemporary culture plucked-up and plunked down into a future setting, a technological extrapolation. We know that governing agencies of prior eras of modernity were largely missing an approximation of today's "growing conscience / guilt-trip" sub-division about having trampled over less advanced / differing human societies[1]. While these new standards are publicly sported about, the global assimilation nevertheless continues, sometimes even with boldfaced glimmers of past methods. But this revision of the West's collective attitude is still emerging, evolving, struggling; so it's premature to predict it won't eventually expunge the "old" and deliver some idealistic Star Trek version of Earth and a Federation. Yet also, take away the interplay with empathy and more brotherly emotional feelings, and reason's progress could just as much output an unconcern for individual rights and "inferior" cultures again. The gist here is that we can't really predict what our own mutable morality would really be like at a superadvanced stage, especially since this would surely concern transhumans and posthumans rather than beings like us.
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[1] Not that alternative groups themselves were really "noble savages" -- in the course of raids, acquiring human chattel, grisly punishments, mass sacrifices, etc., in connections with those no more developed than they. Classic case of mis-associating victimhood with sainthood; like the mixed perceptions that Israeli Jews have conjured.