The moral of the story is, you're a noble fellow if when necessity forces you to commit a wrong against someone, you still feel bad, for a little while at least. But...
The necessity in the story is completely irrelevant to anything in real life, coming from the menace of bad SF figures like the Founders. Like the ticking bomb scenario, the enemy with impossible powers is a premise preselected for a desired conclusion, namely, sometimes you have to be immoral, or dead.
The plotting of how the criminal acts are supposed to save humanity is unbelievable to anyone who has thought about the role of intelligence in the decision to go to war. Again, this is a preselected premise, in this case designed to hinge the outcome of the war on a single person's decision. Maximum ego boo for vicarious identification, in other words.
There isn't a real conflict within Sisko, because the premises make any other choice insane. No, conflict isn't drama, choice
is drama. Sisko has no choice, therefore is not a signifiicant moral agent.
The conclusion is evidently supposed to be ironic, in that Sisko is not really supposed to be able to live with himself. But as an open ended serial, Sisko is able, easily, to live with himself, meaning that the character development in the episode is meaningless.
There's nothing to hate about In the Pale Moonlight aside from its reactionary politics and the absurd praise it receives. It's just another crap SF show.