Well, Libertarianism is generally conceived of as an ideology about
domestic policy -- about how the state relates to its citizenry. The Prime Directive is more an example of non-interventionism -- which is often strongly associated with Libertarianism, but which isn't actually the same thing.
Now, in our own time, it would be considered immoral or wrong to just watch and let one nation conquer and brutalize another.
Oh, nonsense, nations do that all the time.
Let me put it another way, since you're right, actually.
There is generally an outcry when one country brutally oppresses another weaker country--particularly when the weaker country is seen as "innocent". Sometimes nothing is done about it, but at the very least there is a moral outcry.
Our world tends to be inconsistent about whether there is intervention when one power oppresses another.
An obvious Trek example is Bajor-- a peaceful, simple people who are occupied by the Cardassians who practically raped their culture for decades. The Fed did nothing.