What puzzles me more is: How come Mirror Ben exist(ed) in the first place? After all, in our universe, the prophets interfered in order to make sure he would be born.
Actually, I have an explanation for that. A theory, anyway... plus, it would explain why the Prophets didn't recognize him in "EMISSARY".
Remember the end of "ACCESSION"? Kira says it was a shame Akorem never finished that one poem. But Sisko says he did, and shows her the completed poem. Though the timeline was altered, Kira still remembers the old, unfinished poem. Apparently, the Prophets can alter the past without changing memories of the present people.
Since they live outside linear time, when they meet Sisko, they decide to go into the past to make sure he was born. Or very possibly, the 'penance' refers to their decision to do this, since they stopped the Dominion fleet in early season 6 and he doesn't find out about Sarah until the beginning of season 7. His birth would have happened anyway, because Joseph met his second wife only shortly later because Ben always thought she was his mother. But because the Prophets can do things to alter time without actually altering events, Sisko can be born in both universes. This also would explain why there is an Orb of the Emissary now when there was never even a hint of one before.