Hey, I just finished Ex Machina
and am mulling over it a bit before I give a review but I thought it's one of the most interesting and thoughtful analyses of religion we've had in Star Trek. I don't agree with it all but it's a topic we rarely saw handled subtly in the show. I mean, yes, we had Bajor but their discussion of faith was always kind of tainted by the fact their gods were demonstrably real. You don't need to take much on faith when you can use Heaven as an interstellar bypass.
I really like the subtext of the book that religions are evolving things and shaped by countless historical as well as cultural realities. The book nicely skips any of the fantastical elements of religion by simply dealing with the social effect of faith. I felt it was a really balanced view on the subject.
I also think it's a nicely unconventional TOS episode because it's exactly the opposite of the usual sort of thing Kirk does. There's no rushing in and trying to solve everything. It's also a good deal more interesting, to me at least, than the episode it reminds me of (TNG'S "Who Watches the Watchers").
That era's Captain Picard would absolutely love the entirely rationalist Natira and encourage her to continue guiding her people down the path of pure reason. However, Kirk and Spock note that (for better or worse) their religion is THEIR beliefs not something that is easily thrown aside for something shiny but foreign.
(Of course, the circumstances are different as well but Picard's loathing of religion in that episode was pretty clear)
The story is all the more ambiguous and interesting because the faith is demonstrably a false one from a supernatural perspective, too. I thought that made things more interesting too because it becomes a question of the secular value of religion as well as supernatural.
This is some deep deep subject matter I usually don't associate with the TOS period. I'd be interested in what other people thought.