I read in the DS9 Companion that the writers didn't intend it that way and apparently got quite cross when a lot of fans took it exactly
that way. Writer's intentions aside, I also think that this it how it came across.
In the pilot, where the Prophets are introduced, they specifically do not
interfere in the affairs of linear beings; their only desire is to be left largely in peace once they've ascertained that the "invaders" of their home aren't hostile to them. All the more involved Prophet stuff and the whole shebang with Sisko's entire existence being arranged for etc. only got grafted on later as the writers developed this idea; it wasn't in the original concept and to me it never stuck convincingly.
So yes, it made sense that these beings would interfere on Sisko's behalf since they can't afford to have him die, but it annoyed the shit
out of me. There should have been a big showdown confrontation between the two main antagonists, a real back-and-forth fight for control of the station.
Instead when it looks like he's going to lose, Sisko can just call on the aid of some god-like beings who conveniently make an entire enemy fleet disappear. Isn't that just nice and dandy for him. No amount of strategy or strength on the part of your opponent can compete with that.
Lame and unconvincing.