Much of the central part of Rome (including the oldest parts of Vatican City) are constructed from the marble that once covered the Coliseum.
The very earliest Christian churches are built on the site of pagan temples, etc., etc., etc.
Frequently the new buildings for the new religions were built by the former adherents of the old religions, and in many cases, by the very congregations of the old!
There's not necessarily anything "evil" in these discoveries.
What did or did not happen thousands of years ago is irrelevant. Who is butchering whom in today's world is relevant.