If some aliens had done that for the Dinosaurs, we wouldn't be here. See how "Helping" like that can have unforeseen negative effects?
Suppose you go to a party. You see a girl's drink get spiked with a drug and five guys drag the girl to a back bedroom without being observed by the other guests. You check things out. The girl is semi-coherent and weeping and the guys who took her back there are undressing and discussing how they are going to abuse her in the worst ways imaginable. It is in your power to stop this or to allow it to happen.
But, you aren't God and you cannot predict the future.
There is a possibility (for all you know) that the girl will (1) get pregnant with the next Einstein as a result of the impending rape. Or maybe (2) one of these guys is the next John F. Kennedy and turning him in would ruin his political career in which he would have averted a 3rd world war. Or maybe, (3) as a result of the gang-assault this girl will write the most beautiful poetry the world has ever seen.
EDIT: Post Script: Please bring on the Edith Keeler example. I am waitin' for it if you haven't thought of it yet.
Or maybe you act on what you actually know - that a young girl is about to be raped and you have to power to prevent it.
Now, your intervention may have an unforeseen (and unforeseeable) negative consequence. If possibility 2 is correct, for example, then you have doomed the world to nuclear destruction! If you knew this, you might not intervene. But you can't know this, so it cannot reasonably inform your decision any more than any other bare possibility.
The problem of not knowing, cuts both ways. After all, if you intervene, you might unwittingly prevent Dr. Evil from destroying the world too!
The only thing you can do is make a responsible decision given the information you do have. What you have is a pretty obvious violation of this person's rights and a pretty obvious
negative consequence that follows from that violation. That is all you know, that is all you can know, and it is all that you are responsible for.
Again, we cannot assume that the universe within your evolutionary worldview has some hidden purpose and that our intervention will screw up some grand design. There is no design, so at most, our actions may or may not have serious consequences for a happenstance stream of causal effects.
Then again, our inactions may also have dire consequences, so it makes no sense to fret about bare possibilities.
With regard to the dinosaur example, there is no way our alien interventionists could know that millions of years after this impending cataclysmic event humans would evolve. But even if they did, why should they prefer our possible future to the possible future of other species? Suppose the aliens stop the big rock, and the dinosaurs go on their merry way. Maybe some of them even get smart and create a society and culture better than our own. Where is the negative effect now?
The prime directive, in it's weaker form, certainly makes sense. A lot of damage has been done by one culture attempting to help another.
Elevated to the level of an unquestionable dogma, however, it becomes crippling policy of inaction. If it was my daughter at that party, I would hope it was Captain Kirk who saw her get abducted and not Captain Picard who was on that away mission.
EDIT - Post Script: Please feel free to bring on the Edith Keeler example if you haven't thought of it yet.