In the Hands of the Prophets (O.B. 20 June 1993) score: 5

** This episode veers to culture-war, thus the following review may be more contentious than usual. ** 

"In the Hands of the Prophets" might have made a fine episode for later in the series, but as introduction to the day-to-day administration of Bajoran religion -- and thus, to the first extended dialogue with religion in Star Trek history -- it fails.  Behind its pretense of advocating tolerance, we have:

• controversy over Keiko's teaching basic science
• Jake evoking Galileo (the name has added significance for fans)
• Kira's notion of a separate school for Bajorans
• Keiko's schoolroom blown up
• an assassination attempt, by a religious fanatic named Neela (get it?)

Robert Hewitt Wolfe wrote the original script for Season One's finale, and made revealing comments:

Sisko does everything he can not to impose his values on the Bajorans ... (The Deep Space Nine Companion, p. 68)

Actually, no.  As Kira says, a confrontation was inevitable (given the perceived sanctity of the nearby wormhole): Sisko could've sat down with Keiko and Bajoran representatives to draw boundaries.  It may've precluded conflict, especially if Opaka were still available.  Instead, the Starfleeters trivialize local beliefs until they can't, even as the episode paints them innocent. 

Wolfe says the Bajoran heirarchy is based on

fifteenth- and sixteenth-century Catholicism, when the pope held much more of a political office than now ... (every) powerful family in southern Europe was fighting to get their guy to be pope.  (In such a context) Vedek Winn is determined to impose her values on everyone.  

Yes, story and designs evoke the fifteenth century, the better to slam the Christian right, notorious for blocking science, as portrayed.  Like Starfleet's passive aggression, Winn's bullying is very 20th-century.  Granted, Louise Fletcher's Winn became a great Star Trek villain, but her prominence is nearly incompatible with (a message of) mutual religious tolerance.

Religion-bashing (neo-atheism) often exhibits the traits it condemns.  Keiko is satisfying her religious impulse with science: watch her light up as she says the word.  To be entirely fair, this might be intentional character-beat; Keiko is portrayed as rather self-righteous, in this episode.

7 of 9, rapt before the god particle

Religious accounting wasn't necessarily new to the Star Trek franchise.  During Season 2, TOS added John Meredyth Lucas, concurrently writer-producer for Insight, the low-budget dramatic anthology produced by the Paulist Fathers (a Catholic organization).  It's possible this hire was partly to mitigate Gene Roddenberry's insistent agnosticism.*  By 1993, of course, Roddenberry's beliefs were Hollywood-mainstream.

Deep Space Nine's producers supplied an intriguing Bajoran cosmology, only to wander the desert (exceptions will be noted, assuming I continue this blog).  Ultimately, DS9 disposed of its mythology much like The X-Files: extending and attenuating, with switchbacks and red herrings, as many viewers ceased to understand or care.

* I'm aware of no documentation either way (and not having read These Are the Voyages).