The uniforms changed in "Rapture" due to the film Star Trek: First Contact, which came out in theaters between the last episode and this one. In fact, the show had to change to the new uniforms so fast, that initially Ben Sisko's uniform doesn't fit quite right. You can really tell based on the placement of the combadge. But they will fix that by the next episode. And I really like this style of uniform, much more militaristic and dark, very in keeping with Star Trek: First Contact and DS9.
I've always thought there was an unseen ambassador down on Bajor during the middle seasons of DS9. And it was that ambassador that had been busy to make Bajor now (seemingly suddenly) ready for admittance into the Federation. And it's really interesting that THAT (Bajor's admittance to the Federation) is the thing Sisko has to challenge as the Emissary. It really elevated Sisko as a character, that he would make these unilateral decisions even against Starfleet and Federation backing.
What's interesting is that Sisko is choosing to follow the Prophets as their Emissary not only above his Starfleet and Federation considerations, but also above his own life and his own FAMILY. Sisko may be a great family man, but he also understands that some things are more important even than family.
Some of Sisko's character flaws, if you can call them that, is his need for control and his propensity to take thing personal. He actually seems pretty drawn to the idea of being able to see the future, to know what's coming and how to control it. But he's also a good guy, because he's not just thinking of himself; he looks at how he can make it better for all.
Still, I think Jake made the right decision to have Bashir do the surgery to stop the visions and save Ben's life. By that point Ben probably wasn't going to be able to make many more visions anyway before he died, and what good would that do? I think Ben was maybe too close to the issue. He does let things get too personal for him.
Of course, we have to remember that this is not really Bashir doing this surgery. It's the undercover Founder who did detailed brain surgery on Ben Sisko, saving his life but also stopping his prophetic visions.
Perhaps the changeling wanted to stop Sisko's visions of the impending Dominion fleet (locusts). In fact, he might have pushed Jake into it (at least off screen).
It is remarkable, though, that a random undercover Founder would have the medical know-how to perform detailed brain surgery on a human. I guess they really know their enemy.
And he decided to actually use that knowledge vice just letting Sisko die. Wonder what the motivation was there? Do the Dominion secretly like Sisko. Or at least want him to stay in charge of DS9 (versus a new Starfleet officer having to be sent out to replace a dead Sisko). The enemy you know, and all that. Heck, maybe the Dominion actually think they can control Sisko a little better than another Starfleet captain. He does seem to have more faults than your general Starfleet captain. In fact, the Dominion apparently thought they could eventually convince him to betray the Alpha Quadrant for personal reasons and motivations.
Remember Weyoun in "To the Death" tried to offer Sisko power in exchange for the Alpha Quadrant. It seems that the Dominion's psychological profile showed that Sisko's principles could be overcame in the right situations. Well, I think that's certainly true. Just look at Sisko's actions just a few episodes down the road in "For the Uniform". I would say that Sisko violated good Starfleet principles in that episode. But what the Dominion got wrong is that it wasn't personal power that Sisko craves, or that motivates him to betray his principles. But he will "betray" them (or change them or go beyond them) if he feels he's been personally wronged or he feels the ends will justify the means.
We can talk more about Sisko's actions in "For the Uniform" once this review gets there. But I will mention one aspect, since it relates to my thought above. Maybe the undercover Founder somehow caused Sisko's bad decision in that episode. Like maybe he gave Sisko bad info about the probable effects of the poison Sisko used and that made Sisko believe it was a good idea when it really wasn't. And maybe the Founder did try and get Sisko fired after his actions in that episode, just off screen. (This idea doesn't really work because the Founder probably would have revealed himself too much or gotten his "Bashir" self in trouble too. Plus, Bashir wasn't aboard the Defiant in that episode.)