Is that actually true, though? From experience, claims like that are often not based on fact but rather speculation. Given that the Catholic Church led the way in promoting science and rationality from before the time of the Enlightenment (yes, I know many here will disagree!), I'm sceptical of the claim, at least as presented.
So, Church leaders really didn't want to adopt the use of lightning rods, even while knowing the process worked, because they thought God
wanted to zap their churches??? Other than one or two eccentrics, it sounds doubtful. I did a bit of googling, but didn't find anything concrete.
Apparently one of the earliest lightning rods was built by a theologian and used to protect a church:
https://simple.wikipedia.org/wiki/Lightning_rod
Besides the claim of lightning rods causing droughts, others accused lightning rods of causing earthquakes because of the lightning being driven underground. I can't find explicit references to anyone saying "
let the lightning destroy the churches!" They might be there though.