Who Watches The Watchers is not a good exmaple of Picard being dismissive of faith. That example is a straight up misinterpretation, and the only thing Sisko would have done differently is not let Leland arrow him through the chest.
It's not a misinterpretation, and he most definitely is being dismissive of faith.
Specifically, Picard says, "Doctor Barron, your report describes how rational these people are. Millennia ago, they abandoned their belief in the supernatural. Now you are asking me to sabotage that achievement, to send them back into the Dark Ages of superstition and ignorance and fear? No!"
He's not just talking about the idea of them going down to the planet pretending to be gods. He clearly states that rational people abandon their belief in the supernatural. He calls their lack of belief in the supernatural an achievement. There is no other way to interpret that than Picard being absolutely dismissive of religious faith.
Sisko would not have made those statements.