In the Pale Moonlight is a very good episode, but its ethics are wrong on more than the "means justify the ends" angle they went with: said "ends" aren't so noble to begin with.
I mean, sure, as viewers, we can agree that Romulan involvement in the war was in everyone's interests and Sisko is clearly convinced of it as well... but if you examine it critically, is it so obvious? And even if it is, who's Sisko to forego the Romulan right to self-determination?
If the other Alpha Quadrant powers fall, the Romulans essentially lose that right to self-determination. Becoming a Dominion pawn much like the Cardassians did.
They even saw the writing on the wall but allowed distrust to color their judgement.