I too have understood leftism in terms of their subscribing to a sort of "Prime Directive" for a while now. My reasoning and basis for coming to this conclusion ran along different lines than yours (I actually like yours better).
To recapitulate my thinking in this area a bit: I think any analysis of lefty thought has to take into account their millenial utopianism. The future will be utopia; the utopian monoculture will cover the world; this is a given. The only question is, what will be that monoculture be like? Or rather, what current culture will form the seed or root of, and evolve into, that monoculture? Clearly this question must plague most leftists, because they look around, and what is there to root for - especially with USSR gone?
Here's where I believe that the "paradox" you've discovered can be resolved and understood. Basically, the Prime Directive needs to be obeyed because lefties don't like our culture enough to be willing to see it become the future utopia. Other "indigenous" cultures therefore need to be coddled and firewalled because if they are not, lefties know we will swallow them up. This is intolerable not because our swallowing up other cultures will harm those cultures (in most cases they'd benefit) but because then there would be no alternatives.
And the main thing the lefty wants to preserve is alternatives to our society. Why? Again: because he does not like our society.
So, a lefty has a lot of trouble advocating the use of force against even the most vicious of "indigenous" killers. Yes, sure (says the lefty subconscious), we could save a lot of indigenous lives doing it, but look at the down-side: (1) we increase our power and prestige, (2) we reinforce our precedent for "interfering", and (3) we will inevitably influence that culture in our direction.
It's "better" to let other cultures, even vicious/murderous ones, to stay out there, protected from us. Think of it as a sort of extension of lefty thinking on the benefits of "diversity". If each Culture is a member of the Culture-Gene-Pool, then (since diversity is good) it's better to keep them around than to risk them being swallowed up by larger, more dominant (even if better and kinder) cultures!
Hence: the Prime Directive.
Within the context of the Star Trek show, my understanding of why lefties like the Prime Directive fulfills a metaphorical function. The effect of the PD on Star Trek is to ensure that the "Federation culture" is never going to be the only one in the universe. There are always going to be "strange new worlds" to explore, "new life forms" - if a Star Trek viewer had ever been concerned about this, the PD ensures it. This is obviously necessary on a TV show whose main appeal is often the alien encounters. In fact, the humans of Star Trek are often rather boring, so of course a rule to ensure others survive, is a priori a good thing.
Well, lefties, perhaps by definition, think that "our" culture is rather boring (=should NOT be the sole root of future utopian monoculture) thus find it necessary to "protect" others with a PD. Even if this leads to apparent betrayal of their principles.
The betrayal is only apparent because the truth is their principles have less to do with their oft-professed devotion to "human rights" etc., and more than anything else to do with fundamentally disliking their own culture.
IMHO.
But why are Fundamentalist Protestant Blacks, whose religion is at least theoretically the same as that of the "knuckle-dragging neanderthals," treated as something strange and exotic and "other?" Granted, we conservatives often forget that before they were discovered by the radical left they were often mercilessly and cruely persecuted by their "anti-evolutionist co-religionists," but why do today's liberals see something so different from Rev. Jimmy Swaggart's religion? Perhaps it is merely a passing fancy, just as the Left once celebrated (and then discarded) the white Okies of the Dust Bowl days?
Re the idea of a plurality of cultures vs. the monoculture, it is interesting that the European-style "right" identifies the Left with a rootless universal monoculture and call for "multiculturalism" among cultures just as leftists call for it within (Western) cultures. This gives them a certain amount of common ground with the advocates of mystical indigenous nationalism.