You're essentially trying to excuse a large force's persecution, subjugation and displacement of a smaller one to gain access to a natural resource. As a society, we don't do that. As a matter of fact, we tend to condemn it.
Bullshit we don't. We do it all the freaking time and for stakes far less than the Fountain of Youth. You think that if six hundred people were sitting on a cure for cancer in Whogivesafuck, Pennsylvania and the only way to get to it was to burn their town to the ground, that we wouldn't do it?
The Ba'ku were damned lucky that their whitey paradise ended up inside the Federation border instead of inside the Romulan, Klingon or Cardassian border. Those powers would've simply extracted the radiation and left the Ba'ku to a miserable death.