Here's an extended argument. Let me back up a bit to start.
Isn't real drama about looking at something like religion from all ends of the spectrum.
No. There is a species of intellectual weasel who excuse moral cowardice with this rationalization. Making judgments is not the same thing as being judgmental. The Church of Jesus Christ of Latter-day Saints provides an excellent illustration of the difference.
Joseph Smith did not translate the Book of Mormon from golden plates given to him by angels, any more than he correctly translated Egyptian hieroglyphs. A drama about Joseph Smith that shows him receiving the plates or translating in his study is not balanced. Nor is it letting the viewer decide for himself. It is simply dishonest, afraid to offend viewers with the truth. And writing drama where Joseph Smith "might" be a genuine prophet of God is just a stupid effort to have it both ways.
But a drama about Joseph Smith that pretends Smith was uniquely villainous is also false. His followers must refuse to accept simple reason but implying they are any more irrational than any other believers in the supernatural is also false. It would be bigoted to single out Mormons for anything except being more organized and wealthier than other religions.
To avoid this, most so-called drama that takes up religion is pretty much like a drama about love that pretends the stork brings babies! The better writers tend to avoid the subject of religion for this reason?
Obviously many people disagree. They seem to think that religion is like taste. Some people like this and some like that and criticizing religion is like accusing someone of bad taste. Of course, religious thinking informs all sorts of choices and attitudes in daily life. Faced with consequences, some imply there is good relgion and bad. The difference is supposed to be obsvious.
But
no one can say what the difference is other than bad religion justifies things the objector doesn't personally like. They might offer rational justifications for their moral objections but this usually doesn't go far, because religious people don't accept reason as compelling assent---They accept supernatural justifications.
Also, some wiseguy will suggest using the rational moral principles and ignoring the religion! In any event, this moral agnosticism is not wisdom but refusal to commit. What ever is the point of listening to people who just want to evade issues?
Imagining the Bajoran Prophets as functioning as real gods is pretty much like putting "real" angels into your story. It's not balanced or neutral or letting the viewer decide. It's assuming the conclusion. (Good writers could have used them to ask questions like "How do we know the Prophets care about us?" But such things were not an issue for DS9)
In the Hands of the Prophets ostensibly addresses the bad side of religion. The Federation view of Prophets as wormhole aliens metaphorically embodies the scientific understanding of reality. The assumption built into the show is that one could choose to superimpose a religious viewpoint according to taste. In daily life, religion is like a hobby, which just shouldn't have major effects otherwise! (Personally I'm deeply convinced that accepting the supernatural has important effects on your mind.)
The real story is this---Kai Winn organizes an attack on the Federation school for political gain. I can't quite remember whether the assassination of Bareil (I think his name was) was always the goal or an add on. The plot is foiled but Kai Winn lives to fight another day (in the Circle trilogy which I missed.) The plot isn't unfolded this way---and there's other scenes with the Feds, usually making speeches for the validity of religion and against the bigotry of rejecting superstition.
Actually in terms of the show, the school
was implicitly making political criticisms of the Prophets, denying their benevolence and authority! The real meaning of the Prime Directive in Trek's fictional universe is unclear to me. But the real story should have been about the conflict between the truth and what the Bajorans insisted on hearing.
(This is one of those SF shows where you have to ignore what's on screen and interpet it as metaphors for contemporary reality. Personally, I intensely dislike this approach. It combines the inability to write coherent sf with a desire to misrepresent today's reality, truly the worst of both worlds. By the way, writers who claim science and religion are compatible would be more believable if they were not only incredibly ignorant of science, but boast of their hostility to science!)
In other words, the story is about how a nasty politician/clergyman whips up a storm over teaching of evolution (best real world topic) to gain political points. And he's using it as a cover to assassinate a rival politician/clergyman when he comes to defend the evolutionists!
Now lots and lots of believers have absolutely no need of a clergyman or a politician to get upset over evolution. The insult to their vanity does that. It is the politicians playing demagogue who pander to that indignation, instead of creating it. It is rarely in the interest of politicians to be seen as causing public disorders. It is also rare that
powerful politicians resort to violence. Riots, bombings and assassinations are usually the resort of the weaker parties. There is rarely a political or religious leader who can or will calm the mob (at the moment I can't think of any! Ever!) And the bigotry most certainly does not conveniently disappear after the evil misleader is unmasked!
That's just not the way that things are. It's not even a story about what might be! The story shouldn't have been judgmental, casting the Bajorans as benighted fools. But as it is, the story pretends that the Bajorans who thought demoting the Prophets to wormhole aliens raised questions about why they should be obeyed are just being foolish. Despite all the palaver about toleration and equal treatment of religion, the story still assumes that people who take their religion seriously are sheep! I think they're wrong. But I think that view is really more respectful of them as people.