There is one thing I never understood about this arc, even if it was well written - why the hell did Sisko care if Eddington duped him?
I see it as the darker side of Sisko's committment to his command, his crew and his mission: he takes betrayal very seriously, and he considers Eddington to be his responsability.
It's not especially admirable, but that is intentional: DS9 does not always portray its characters in an heroic light. I suppose it would be better if Sisko could approach the situation in a completely objective manner, but the fact is that he can't, and that is perfectly plausible: he was Eddington's commanding officier, he trusted him and was completely duped by him, which allowed Eddington to make off with some industrial replicators that he will put to good use presumably (also, in the end, Sisko's responsability).
Sisko's obsession with Eddington is certainly a flaw, but a believable one, given what else we know about Sisko's personality.
EDIT: I will say that one criticism I would make of how Eddington's betrayal is handled is that it comes too long after the character was introduced, to the point where he doesn't seem to be much more than a glorified extra, rather than an important member of the station's crew. RHW confirmed at some point in online chatter that Eddington was intended to eventually become an antagonist when he was originally brought on board in
The Search at the beginning of season 3. His next important moment comes later that season in
The Die is Cast, when he sabotages the Defiant's cloaking device (a hint of things to come). It's at this point that Sisko tells Eddington that he has never doubted the word of anyone wearing that uniform, and decides to go on trusting him despite what just occurred. It's partly these events that spur Sisko's anger at Eddington's eventual betrayal, but the writers don't get back around to having the betrayal actually occur until late season 4, at which point Eddington has faded into the background for almost a full season. The setup for this arc could have been handled better. Basically, there is too big a gap between the events of
The Die is Cast and
For the Cause.