The events of In the Pale Moonlight wouldn't have the same dramatic weight if they took place in any other series. It has to be a series like Star Trek which has such high minded ideals. Without those ideals, what Sisko did wouldn't be shocking or controversial.

Lets review, bribing a Ferengi, selling biomemetic gel, being an accessory to murder, forgery and fraud. But its all in the service of fighting an existential threat to your homeland.

If this were, say, a James Bond movie, there would hardly be anything controversial about this (maybe the biomemetic gel or whatever the equivalent would be). Indeed, this would be quite dull and we'd be asking for violence and gadgets and stuff to be thrown into the story.

But in a Star Trek story, all of this violates Federation principles and gnaws at Sisko's conscience. That's why he's making the Captain's log throughout the episode. That's why he has to tell himself at the end, has to insist at the end, that he can live with it.

To me that means In the Pale Moonlight is every bit a Star Trek episode in spite of its controversial nature.