Mr. Laser Beam wrote:
The very fact that S31 is not accountable to the Federation makes it impossible that they could possibly put the interests OF the Federation ahead of their own.
Impossible? S31 is a part of the Federation, it's agents (most of them anyway) are from among the Federation's population. Its aims were not simply for the benefit of the small number of people who composed S31, but for the Federation as a whole.
You might not like the tactic of biological warfare against the Dominion, preferring conventional methods, but the S31 plan of introducing the sickness into the Founder population is what ended the war in the time frame we saw.
Conventional warfare very well could have eventually ended the war in the Federation's favor, but the war would have been longer, and resulted in the Federation (and it's allies) experiencing more causalities and destruction.
Regardless of any "unaccountability," S31 saved lives. And yes they poisoned, and kidnapped, and lied, and who know at some point they might even have taken candy from a baby. I don't think anyone is going to claim that these are nice people. It isn't a case of putting the Federation ahead of themselves, they are a part of the Federation.
However, it would be fair to say that S31 put the Federation ahead of the Dominion.