The fact of the matter is that on a given world, the various nations upon it influence each other, either directly or indirectly. Did you know that there are native cultures living in remote regions (like the Amazon region) that have no clue about the modern world outside it? That they do not have contact with technologically equipped humans? They are interesting examples of
"primitive humans". They've been pretty much left alone because of biology (we are carriers of diseases that our immune systems keep in check, but would devastate these people because they have no immunity). There has been some contamination, via accidentally dropped air cargo (see "
cargo cult"). Do we intervene and help them progress, or leave them alone? Very similar to this "prime directive" concept. (click
HERE for an interesting article about encountering a remote Amazon tribe).
There are two main reasons to intervene:
1) The species has advanced to the point where they would easily survive the shock value of being visited by extraterrestrial beings. They are made aware and given the choice of whether to remain isolated or join the Federation.
2) A species showing much promise* or positive potential is suffering from a catastrophe that is not too difficult for the observing beings to correct.
* - what really constitutes "promise"? That's the difficult point to ponder. Is the species stagnant in their ways, or perpetually continuing conflicts with other inhabitants of their world? It has to be determined on a case-by-case basis.
Eventually those remote natives on Earth will find themselves at the doorstep of the modern world. Do we build a wall around them or do we invite them in? Do we allow our contamination to eventually kill them (and it will), or do we deliberately boost their immune systems to make them compatible with the world? If we're able to communicate and then fill them in gradually... "Hey, you've been living in an isolated part of the world. We have a huge global community. If you were to be a part of it, there are a number of things you must do (A, B, C... X, Y, Z). If you are OK with that, let us know and we'll help you adapt." They think about it, then in a few months we contact them and they want no part of it. That is their choice. But unless they are OK with staying within a predefined "reservation" zone, they will bump up against our community and be contaminated. Disease, bacteria, and viruses will get to them and many will perish, because of their unwillingness to adapt.
Separate worlds are a different story, though similar. A planet has its own independent biosphere. If the indigenous beings remain planet-bound, they'd never even know an external multi-species community existed. But... what if they were on the edge of the Romulan Neutral Zone? Or Klingon Space? Those species do not have any Prime Directive policies... Do we warn them of the dangers? I believe they have that right to know, even if it means disrupting their community (it will eventually be disrupted anyway, and in a way where they have no choice in the matter).