I think I like the aired version better in most of these cases.
I think the Honor Among Thieves idea sounds like more of an Analyze This vibe than a Goodfellas vibe and would have made the Orions more like a slapstick version of the mafia instead of a mafia to be frightened of.
And if O'Brien was actually a Cardassian agent it would have been like the Bashir genetic twist and cheapened everything about his character, adding a gimmick to a gimmick-free character. Also I'm not sure how they would have explained Molly's silverware-free forehead.
I do like the idea of Kira being an addict, it would have jived well with her past.