Both were ends justify the means scenarios. Both Sisko and Anakin were tempted and gave into their dark compulsions with the promise of greater rewards by someone. One is a master of deceit who prides himself on manipulation and telling half truths with the power of suggestion to achieve his goals and the other is a sith lord. We saw both Sisko and Anakin weigh the options of their decisions and chose their own selfish desires. While Sisko's was indeed for a nobler cause when compared to Anakin. I think the body count for Romulan casualties outweighs the Jedi casualties cause by Anakin's betrayal. Comparing Anakin to Sisko in this way I find interesting because in Ep III we see Anakin go from a brave knight to evil bastard. One decision and Anakin slides further and further down the silppery slope "Into Darkness". With Sisko we get the same line every other Captain, Admiral and even Section 31 members utter " it's for the Federation" . So I guess that makes it ok.