I think the issue in this episode was less a moral issue and more a 'Feeling like a huge dick' issue. It would have served their manly pride better to win a glorious battle against the Gem'Hadar who they respect as warriors and opponents. Sisko just reminded them, screw pride and sportsmanship, this is war.
There are rules in war. Legal treaty or not. Like no torture, no genocide, no random targeting of civilians. Exploiting a tactical advantage does not violate any of those rules.
1) Dead right on the first. Ruses of war are specifically legal by our own actual laws of land warfare. This one involves a Dominion collaborator sending his troops into a trap, but that's permissible. Had Sisko and the rest attempted a false surrender, that would have been an impermissible ruse.
Article 37 of the 1949 Geneva Conventions forbids killing enemies perfidiously. Perfidy is defined in the Conventions as "acts inviting the confidence of an adversary to lead him to believe that he is entitled to, or obliged to accord, protection under the rules of international law applicable in armed conflict, with intent to betray that confidence."
If we're looking to rules we do have and know, here on earth, then here it is: Sisko and his group were not breaking any rules. Ruses, stratagems, ambushes, using collaborators as defacto spies, all these are just fine.
2) I don't know where this "no genocide" business comes from. In an us vs them situation, if genocide is the only way that your side can survive, then you do it. If the choice is "we die (or are enslaved, or have our civilization obliterated, etc) or they die, no other options," then there is NOTHING wrong with making the choice, "they die." At all. And if that end requires that an entire enemy gene pool be annihilated, then that's what it means. Section 31 was not wrong in unleashing a disease on the Founders (and note that they did not target the Jem'hadar or Vorta; just the species that had to go to bring down the Dominion).
