The idea behind it is that by that species becoming extinct, a new, more intelligent species may arise. So while you may be saving one species, you might be preventing the appearance of another, also, because no other species will evolve to intelligence if there is a dominant species on the planet already. That's why the Prime Directive is about non-interference, and not about saving/not-saving a civilisation. You don't interfere, and what happens happens.
I think it is liberal to suggest that the act of one person or one ship's crew could significantly alter changes that have been developing for a long time (remember: quantitative change results in qualitative change). At best they can only delay the changes.
Of course, the counter to this claim is that people must be protected at all costs. Prime Directive is easy when it's people vs. nature, then you side with people and problem solved. But what if it's people vs. less developed people? Whose side do you go on then?
Admittedly, I don't remember the details of the episode, but TNG episodes with these kinds of questions are more about starting a debate, rather than moralising or telling you what to think. They present a problem, and because it is a TV show it has to have some sort of resolution, but that doesn't mean your conclusion at the end has to be the same as yours.
What about that Picard's decision not to genocide the Borg? What do you do then? Do you kill a whole species because they are "evil"? No, that would be liberal moralising. You kill them all because their internal organisation and their structure/way of life necessitate destruction of other life. But Picard let's them live… in a very liberal move. Damn, it's like appeasing the fascists. Then the Borg come back and kill a bunch of people.