I suspect there's even more to the story than what is apparent in Darwin's anecdote, both because right or wrong it simply doesn't fall under the category of heresy, and given that metamorphosis had been a well observed and documented phenomenon for hundreds of years prior to the event. For example in De animalibus insectis libri septem by Ulisse Aldrovandi[1][2]

It may even be in the order of thousands of years even though we don't have written accounts of it, given that's how we have practiced apiculture and had the opportunity to closely observe the phenomenon. And apiculture has been widely practiced by monasteries, so churchmen should not have been entirely unfamiliar with the concept.

1. https://archive.org/details/deanimalibusinse00aldr/page/280

2. Coincidentally Aldrovandi was also accused of heresy, but for anti-trinitarianism, not for describing metamorphosis: https://en.wikipedia.org/wiki/Ulisse_Aldrovandi#Heresy