First off, he was not reluctant to meet Opaka. He met with her pretty much right when that Vedek came to him and said, "It is time." When he became known as the 'emissary', of course he would want to distance himself from that role... as a Starfleet officer, he is not supposed to interfere in the internal affairs of another world. If he actively did things in the role as emissary, he would very much be affecting Bajor. That's wielding a massive amount of power because, let's be real here, super religious people tend to be led like sheep when someone they view as a religious icon says anything. No one should wield that kind of power, and Sisko actively tried to avoid having that power. (He later did accept the role, but he only interfered once... in "RAPTURE".)
Second, he was never dismissive abount the Bajoran belief. He respected that it existed, but he wasn't going to be a follower. It IS possible to not agree with someone's beliefs in certain things and actually NOT be a member of the 'other side'. Unfortunately, a certain segment of the population doesn't seem to understand that notion.
Third, he didn't want Nog around Jake at first because the first thing that happened when Sisko arrived on DS9, Nog got arrested for stealing. Would you want YOUR child hanging around a criminal?
Fourth, while he did say that Ferengi and humans didn't have a lot in common, he DID change his mind about that fairly quickly. We see the first hint of that in "THE NAGUS" when he watched Jake teach him to read. That was in season 1, by the way. And he endorsed Nog's Academy entrance, which was season 3. If I understand math correctly, the numbers 1 and 3 come before 4. Hence, this was before season 4.
Fifth, he had disdain for Quark because Quark had caused trouble on DS9 multiple times.
"BABEL" - he got the disease spread everywhere because he broke into quarters to use the replicator.
"THE PASSENGER" - he brought mercenaries to help steal a Federation tanker.
"MOVE ALONG HOME" - he cheated the Wadi, and they went through the whole ordeal due to this.
"VORTEX" - he tried to double dip with Croden and got the Miradorn twin killed.
"THE SIEGE" - he was selling seats on evacuation runabouts that were meant for civilians to get out to safety.
"INVASIVE PROCEDURES" - he bypassed security sensors and Verad's group nearly got Jadzia killed.
There are other examples, but I think you get the idea why Quark was not at the top of his Christmas list.
Sixth, Picard - he represented the biggest loss in his life, Jennifer's death. You're going to have residual feelings for a while after that. You can't just shut off those feelings. Especially at that time, when they didn't know as much about the Borg and what they do to the assimilated. He got past that grief and anguish by the end of the pilot episode.
Did Sisko have flaws? Absolutely. Did he grow past many of them? Definitely. Was he a layered captain? BY FAR, he was the most layered captain because he had flaws, and got past them. He was human, and humans make mistakes and do the best they can with what life throws at them.
Calling Benjamin Sisko a piece of shit is like saying ALL humans are pieces of shit. And while a lot of people today are because they don't try to grow and learn, Sisko NEVER belonged in that category.
Finally someone who has common sense and logic. Took the words right out of my mouth, well in this case my mind. I almost thought I wrote this masterpiece and had just forgotten about it.