This is season one, logically over time O'Brien would work the kinks out of the system, get used to working with the Cardassian tech, and improve the station's interface with Federation technology, that sort of thing.
It's similar to the improvement in Federation shield technology noted by Weyoun when the Dominion attacks the station in Call to Arms at the end of season 5. We can infer that this improvement was achieved due to intelligence gathered from the Jem'Hadar vessel salvaged in The Ship (and perhaps other, similar discoveries), though this is never explicitly stated.
It makes sense that O'Brien's familiarity with the Cardassian tech would increase over time and that this type of issue would no longer occur. The station still holds some dangerous secrets as late as Civil Defense, but once the weapons systems are upgraded in Way of the Warrior, I don't think the station itself poses any further problems. There's no reason why it would, really, since Starfleet engineers would certainly smooth over any outstanding problems the longer they worked on the station.
EDIT: O'Brien actually specifies that the "root canal" or full overhaul of the station's computer systems would take 2 or 3 years, which means it might well have been completed not long before Way of the Warrior, though I doubt the writers had a specific schedule in mind.
"ITPM"?
