It never bothered me. I thought it was pretty clever really. Ira Behr said the following in the Companion:
"I felt it was the perfect next step in the evolution of the relationship between Sisko and the Prophets that began in the pilot. Hearing people refer to it as some dopey deus ex machina is really annoying because I would think they'd give us more credit for being on the ball. We didn't have to end it like that, we chose to end it like that. Because we wanted to say that there was something going on here. And ultimately, that would lead to our finding out that Sisko is part-Prophet. They wouldn't have done this for just anyone. This was the man going out into the wilderness and demanding God to interfere, to do something for crying out loud. The corporeal characters had done so much in the episode; surely they'd earned the help of the gods."
I agree. When you add godlike characters to the mix, you
demand godlike actions and this one worked--sweaty palms and white knuckles and all. What did not work was the way WYLB handled the end of the war of the gods and its a shame, since it could have easily piggybacked on this moment. What if Dukat had access to those ships? As he and Sisko duke it out (perhaps across realities, one of which including Benny Russell's), we are aware that, if Sisko loses, the Dominion floods the Alpha Quadrant and everything goes to hell. That way we get one huge battle that ends both conflicts rather than a really cool end of he Dominion War followed by a really lame end of the Prophet's War and even lamer use of flashbacks.