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.
That's the problem with the Prophets. They see all time as one. They now understand that corporeal beings see the past present and future, but that doesn't change how they see things.
They should have known the Dominion fleet was going to come through the wormhole and that the only way to save their Emissary was to destroy the Dominion fleet.
From our prospective it looks like they came to their decision at that moment, but if they truly see all time as one, their decision was made long before.
They talked about Sisko following a new path. More strange talk from a set of entities that see all time as one. Their was no new path, it was the one they knew he was going to take. They were f**king around with him, telling him his Pagh will follow a new path. They knew they were going to destroy the Dominion fleet. They knew they were going to bar the Dominion passage through the Wormhole. Yes it was never actually said but it was implied as no other Dominion fleets or ships tried to come through.
Sisko made no argument they hadn't already heard. They interfered because they were going to. Everything they did they did because they were going to.
They allowed the Dominion fleet into the wormhole because they were going to destroy it. They knew the path Sisko would take, they never changed it. They knew they could not stop the Pah Wraiths from taking over the Wormhole, so they sent one of their own out to not come back until needed.
They were written as all knowing, yet caught by surprise?
So since they knew what was happening, what was going to happen, that they would interfere does make it a Deus EX Machina. They were going to stop the fleet, no matter what because they saw it already.