In a (lame) season 1 episode, Sisko is told by Q that "Picard would not have done that" only to be punched and told, "I'm not Picard." Well, this episode goes far and beyond where Picard would have gone. (Though I suppose "I Borg" could cast some doubts on that.) Picard was an obstinately ethical and by-the-book guy - someone who would break the rules on occasion, but act honorably and morally even if it cost him and his colleagues... and the Federation.
Sisko had already pushed this boundary in earlier seasons, but here irrevocably crosses the line. In fact, the line between villain and hero is blurred quite aggressively here - you could easily write this story with Eddington and Sisko's roles reversed. And it's even worse because Sisko's pursuit of Eddington has a pretty big personal vendetta behind it.
We'd have one last encounter with Eddington later in season 5. A worthy adversary!