They were never on a mission together during the time they were married, except in that instance.
They shouldn't have been assigned together by Kira in the first place, but to be fair, they were the highest ranking Starfeet officers on the station at the time, and time was a factor. Given the highly secretive nature of Lasaran, it's very likely only officers with a certain security clearance level high enough could be assigned. Both are Lt. Cmdrs., which is high enough, I'd say, for a LOT of things.
I don't think Sisko can be faulted here, even incidentally. And he DID give new orders that they were never to be assigned together again.