I simply do not think saying belief in such stories are or the equivalent of religious beliefs.
False dichotomy. Belief is belief. They're only different in that the adults who told them these things "know" they're different. From the perspective of the children, however, there is no difference between a belief in fairies and a belief in God. In both cases, they are defending perspectives they "know" to be true.
Regardless of the children's awareness of the underlying truth of the beliefs, the importance of the belief in question should, IMO, be factored into how the discussion is treated.
I would not want my child's teacher to treat belief in the divine as if it were on the same level as belief in fictional fairy stories. Even if the teacher believes that my religion is tantamount to fiction, the importance other religious belief/non-belief is assigned in the reasonable person's life should afford it greater respect than a difference of opinion on other matters, like the existence of fictional creatures.
I would have wanted the teacher to acknowledge that fairies are imaginary creatures, but that it is perfectly acceptable to engage in pretend play that they're real. For a difference in religious opinion in a multi-faith environment, I think along the lines of blackcat. In a single-faith school, I'd want a message consistent with the beliefs of the religion.
