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The episode of DS9 I mentioned, had a theme to it I found horrifying - that there are different 'sorts' of people and you couldn't change them so don't try. I doubt the writers were going for racist subtext, but you must be able to see how it is, probably unintentionally, there?
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I remember reading a sci-fi book that had a sort of complement situation to this one. It had a plot sort of as follows:
There was a human colony on another planet that also had it's own indigenous intelligent race. For whatever (stupid, IMO) reason, the human nation had a treaty with them, which subjected the human colonists to their byzantine laws whenever they interacted with them. The usual penalty for any number of trivial "offenses" was for them to take custody of your children.
After that, they'd force-fit the human children into their culture, even going so far as to re-work their appearance and senses. The result were twisted psychological wrecks whenever they were outside the conformative pressures of the alien culture. Lesson: humans were never psychologically built to be faceless, nameless, perfectly interchangeable units who would never
dare to call attention to themselves as individuals.
And maybe humans are psychologically adaptable enough to be force-fit to such a situation and still manage some sort of survival. But it usually takes guns, barbed wire, and trauma to do it, so maybe it isn't the best idea.
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It may not necessarily be racist if you really are talking about a different species (and one that has less in common with you than a mutant sea anemone at that). Maybe intelligence is more general than the biology that gives rise to it. But it's possible that even intelligent personalities take a lot of their driving forces from genetics, and can't be pushed indefinitely outside their nominal operating parameters, and thus aliens would have cause to be somewhat alien.
In addition, some people, for reasons that have nothing to do with their race, have a certain specific personality that can't be permanently altered to any arbitrary degree.