I don't think so, simply because it wasn't just something that happened out of the blue and was never mentioned again. As others have pointed out, they specifically showed on numerous occasions that the Prohpets could interfere with corporeal matters and had been doing so for some time.
It's also worth considering I think, that Sisko didn't simply ask and get what he wanted. It came with a price, which the Prophets came looking for when the time was right. He had to pay for their help and in doing so, was separated from his family and friends.
So it's not like the Prophets stepping in to save the day, was completely out of the blue and had no lasting effect. For me, if the prophets had never been mentioned or never gotten involved in anything before then, and the moment of facing all those ships was the point of their discovery and Sisko was able to convince them to get involved, and then they never returned to do anything ever again....that would have made it a Deus Ex Machina.
That's not how it played out though and as such, to me at least, it felt natural....at least as natural as non-linear wormhole aliens suddenly making 2800 Dominion ships vanish into nothingness, possibly can be.