Since contamination by a single species (especially a sapient humanoid one) often happens yet never kills a world in Star Trek, it follows that the decision to move the Boraalans was safe and sound in that respect. Whether Star Trek is realistic isn't really an issue here, because the safety of the Boraalan transfer is inherent in the show format where all the myriad humanoid species and Earths are perfectly interchangeable. Any attempt at inserting "realism" in this respect would collapse the entire story format.
Besides, for a small group of Boraalans to kill a planet, even the darkest "realistic" scenarios would involve timespans of several generations. Plenty of time to amend the situation afterwards. The minuscule group of Boraalans would not notice any of the amending anyway, as they would only cover and control an insignificant fraction of the planet and would have no means of observing the rest.
What Nikolai did here was comparable to what Kirk did in "Paradise Syndrome", except he didn't reveal forbidden things to the natives quite as much. Any later corrective action would also be comparable to that episode. The argument really is which of these episodes is the greater mystery, the greater divergence from the Star Trek norm on dealing with ignorant natives in mortal distress. Both are extreme cases with seemingly absurd underlying premises...