Why wasn't Sisko replaced?

[Tosk]

It reflects a maturing of Sisko and a greater amount of trust that SF has in him, something not reflected in the pilot.

How does it indicate those things? Whatley warns Sisko that he could have his commision for going against the mission statement, and that the only reason he wouldn't risk it being that they would probably lose Bajor forever. The only source of info we have on the situation says that it's Sisko's role as Emissary that saves him, not increased trust from Starfleet.

I still don't see what it is in the scenes in Emissary that fuels this claim that Starfleet has no faith in Sisko, or that he was a slacker or putting in a poor performance or whatever. I acknowledge it's possible I'm missing something obvious, which is why I keep asking for specifics.

 

[Noname Given]

Picard made it sound pretty important to me.

PICARD: I'm a strong proponents for their entry into the Federation.
SISKO: Is it going to happen?
PICARD: Not easily. The ruling parties are at each others throats. Factions that were united against the Cardassians have resumed old conflicts.
SISKO: Sounds like they're not ready.
PICARD: Your job is to do everything short of violating the Prime Directive to make sure that they are.

Which part of the conversation is that from? The only vibe I catch from Picard is his annoyance with Sisko's attitude towards him personally.

To be fair, Picard can make a normal bowel movement sound important (Well, it's more how Stewart delivers ANY dialogue he's given. )

 

[Bad Thoughts]

Whatley warns Sisko that he could have his commision for going against the mission statement, and that the only reason he wouldn't risk it being that they would probably lose Bajor forever. The only source of info we have on the situation says that it's Sisko's role as Emissary that saves him, not increased trust from Starfleet.

Let's not paraphrase too much. Whatley does not order, but he strongly requests that Sisko reverse himself. He suggests he could take Sisko's commission. He acknowledges that because of Sisko's religious position, that doing so would have adverse consequences. And then he accepts Sisko's recommendation as Starfleet officer and Emissary. By this point, Sisko has greater standing than when he was in front of Picard: Whatley is willing to allow the policy to be modified at Sisko's recommendation. The Bajorans aren't ready.