Well, I saw Rapture (possibly my favourite DS9 episode -- despite not being a spiritual person myself, seeing Sisko become a true believer because of the gift of his vision and the consequences of it I found thrilling -- the grand moment where he derails the Bajoran-Federation membership talks was amazing) as a big turning point for the character and Reckoning as being a logical extension of it, though I will concede he didn't have a Bajoran-like devotion to them; given what we know about his nature, that makes a lot of sense.
"Rapture" is one of my favorites, too. But I interpreted it a little differently than you did.

I very much like the fact that he hasn't rejoined Starfleet in the novels -- that would seem out of character given the journey he's been on.
Sisko is still in Starfleet. He's just on family leave.