Its a concept that Gene Roddenberry refused to accept, that Rick Berman and co. embraced, Even in 400 years time, during a major crisis, Humans will resort to questionable measures, if it means a "greater good" will come out of it, thats exactly how Sisko justified his decisions in "In The Pale Moonlight"
Even though not explicitly mentioned "The Needs of the Many, Outweighing the Needs of the Few" is more or less quoted by Garak, when he tries to reassure Sisko that his actions in the "Romulan Accident" were justified
If Sisko hadn't done what he did, the Dominion would likely have conquered the Alpha Quadrant, the Romulan Empire considerably strengthened their forces and saved millions of lives
Another controversial point, that has its basis, is Section 31's "Changeling Disease", technically Section 31 were responsible for ending the war, by Odo curing the Female Changeling and then promising to cure the rest of their Species, the Female Changeling in return surrendered and the war was officially over, sure the combined Starfleet/Klingon/Romulan and Cardassian forces may have all but obliterated the Dominion's Alpha Quadrant presence, but what was stopping them from eventually returning? after all the Dominion can build forces in a rather short time, they could have retreated, rebuilt an Armada and returned a year or so later, just as the Alpha Quadrant was beginning to rebuild and recover from the War
Even though not explicitly mentioned "The Needs of the Many, Outweighing the Needs of the Few" is more or less quoted by Garak, when he tries to reassure Sisko that his actions in the "Romulan Accident" were justified
If Sisko hadn't done what he did, the Dominion would likely have conquered the Alpha Quadrant, the Romulan Empire considerably strengthened their forces and saved millions of lives
Another controversial point, that has its basis, is Section 31's "Changeling Disease", technically Section 31 were responsible for ending the war, by Odo curing the Female Changeling and then promising to cure the rest of their Species, the Female Changeling in return surrendered and the war was officially over, sure the combined Starfleet/Klingon/Romulan and Cardassian forces may have all but obliterated the Dominion's Alpha Quadrant presence, but what was stopping them from eventually returning? after all the Dominion can build forces in a rather short time, they could have retreated, rebuilt an Armada and returned a year or so later, just as the Alpha Quadrant was beginning to rebuild and recover from the War