While I find all of the acts morally questionable, the one that I find to be the worst is Sisko poisoning the planet.
I agree, that and the Klingon ruining a whole biosphere just to keep Picard from recovering the DNA fragment were global scale. Phlox also aced badly--the old species could have been relocated perhaps. Lastly, Spock' forced mindmeld of Valeris was definately of the Gitmo/waterboard variety--and yet still had to be done to avoid something worse Inglorius Bast**d style.