And this is why DS9 sucks. It basically calls the Federation a lie; the victory requires abandoning the morals. In TNG this would not have happened. The victory would have been won by rejecting S31, and gaining the respect and trust of your enemies. If the Founders could not have been reasoned with, then it would have been about making their subject races to realise that they don't need to be slaves.
I disagree that it calls the Federation a lie. It just exposed that there is a price to pay for the utopia of the Federation. The ideals of the Federation do not keep the Fed from engaging in wars, but what happens when the opponent does not play by the rules of the Fed? We see a real world example of this with terrorism. There are rules of war, rules of conduct set forth by the governments of those armies. Terrorists do not recognize they rules, nor do they play by them. So, when fighting a terrorist, one can either bend the rules to even the field, or stick a moral code that doesn't exist for the terrorists.
Did you ever see 'A Few Good Men'? I think Sisko understood this in a way Picard never could.
"Son, we live in a world that has walls, and those walls have to be guarded by men with guns. Who's gonna do it? You? You, Lieutenant Weinberg? I have a greater responsibility than you can possibly fathom. You weep for Santiago and you curse the Marines. You have that luxury. You have the luxury of not knowing what I know, that Santiago's death, while tragic, probably saved lives. And my existence, while grotesque and incomprehensible to you, saves lives! You don't want the truth, because deep down in places you don't talk about at parties, you
want me on that wall. You
need me on that wall. We use words like "honor", "code", "loyalty". We use these words as the backbone of a life spent defending something. You use them as a punchline. I have neither the time nor the inclination to explain myself to a man who rises and sleeps under the blanket of the very freedom that I provide, and then questions the manner in which I provide it! I would rather you just said "thank you", and went on your way. Otherwise, I suggest you pick up a weapon, and stand a post. Either way, I don't give a
damn what you think you are entitled to!"
I think the Star Trek universe is better for having both Picard and Sisko. Picard for being the idealist, the dreamer, the great negotiator and Sisko for being the the realist and realizing that sometimes loosening your moral belt is worth it to save billions of lives.