In The Burrowers Beneath we find out the Wilmarth Foundation and some other allies of Crow have been performing experiments on young Chthtonians in order to figure out how to kill them. They've also destroyed newly hatched ones. Later, we discover the Elder Gods are the "good" versions of Cthulhu Cycle Deities. Does this mean our heroes have murdered a bunch of innocent babies?
Depends how much of a Hive Mind the Chthonians actually have, and whether or not the CCD specifically engineered their kind to be innately evil from birth.
The Cthulhu Cycle Deities awake during the events of Elysia and during their brief time awake, destroy the titular planet. We never find out what happens to Earth during this time but it's very possible the Great Old Ones utterly laid waste to it during this time period. Titus Crow and Henri pointedly never mention what happened to it, and we only have secondhand word that the CCD were too focused on attacking Elysia to bother laying waste to anywhere less significant.
We never learn just how severely Arkham and Miskatonic University were damaged when the Foundation's headquarters there was attacked in retribution for taking a shot at Cthulhu's daughter.