I was recently rewatching Star Trek: Deep Space Nine, and in particular, the episode Tears of the Prophets (Season 6, episode 26). A major plot point in this episode revolves around former Leader of Cardassia, Gul Dukat, attempting to find a way to bring in Dominion reinforcements through the wormhole. In particular, Dukat releases a Pah-Wraith from a small figurine and subsequently becomes possessed by it.
What is interesting, however, is that Benjamin Sisko receives a vision shortly before this from the atemporal prophets warning him that Bajor is in danger:
[Ops]
WORF: The Sisko is of Bajor.
[Wardroom]
MARTOK: It is where he belongs.
[Captain's office]
ROSS: It is where he is meant to be.
SISKO: Are you telling me not to go to Cardassia?
[Ops]
ROSS: The Sisko is of Bajor.
MARTOK: It is dangerous to walk a different path.
SISKO: Dangerous? In what way?
ROSS: The Sisko must not leave the chosen path.
WORF: The Sisko is of Bajor.
LETANT: It is where he belongs.
SISKO: Why is it dangerous to leave? And how will it affect Bajor? You have to tell me.
(The vision ends.)
This is routine for Sisko, being emissary of the prophets, but much more surprising is Admiral Ross's response to the vision:
SISKO: The Prophets don't see me as a Starfleet captain. They see me as their Emissary.
ROSS: That's the problem, isn't it? For the past six years you've tried to be both, and up to now I've been patient. I've indulged you, I've gone out on a limb for you many times, but this is it. You've got to make a decision. You are either the Emissary or a Starfleet captain. You can't be both.
In which Ross tells Sisko to deal with his conflict of interest. The problem with this statement is that not only is the Bajoran religion demonstrably, provably true, but the prophets are instead instrumental to the outcome of the war by preventing Dominion Reinforcements from coming through the wormhole!
In this case, the logical conclusion is that the 'Emissary' of the prophets is certainly an extremely valuable strategic tool for the Federation to hold, and one that they never use and actively refrain from encouraging.
Why does the Federation not attempt to use the prophets to their advantage? Is it because Bajor is not a Federation planet and has a non-aggression pact with the Dominion or due to some ramification of the prime directive?