Was this indeed a subtle dig at religion and the labelling of it as essentially mere fable rather than fact as so many accept it?
It could be read that way--or this single line could be boiled down to be nothing more than the result of "alien misconception" by the Keeper--thanks to references to religion (and we can assume, its associated text) as something accepted / believed (usually Christianity) by characters in the regular series.
Examples: McCoy in Act 1 & the final Kirk/Uhura bridge lines from "Bread and Circuses,"
or "We find the one quite sufficient
from "Who Mourns for Adonais"
(as a counter to apparently false "gods" of myth). I would add, Daystrom's "Murder is contrary to the laws of man and God
" stands as more evidence of the continued belief.
Further, some love to use the "Kirk was always tearing down gods" line as behavior suggestive of rejection/disbelief, but if one considers the quoted lines above (particularly his comment/relationship to Apollo), then we could take his efforts as meaning he does not stomach frauds--behavior echoed in The Final Frontier
with his questioning of the entity.
There are more TOS examples, but for anything which could be read into the Keeper's single line, it failed to establish a pattern of thought / approach for the regular series.
Note: the Keeper also had a total misunderstanding of humankind's rejection of slavery/breeding programs. This would support all other clueless Talosian observations--including the "fable" idea.