The point of a public stoning is that everyone in the crowd has to pick up a rock. It is a team building exercise.
One progressive way of reading the history of the world is as a story of the successive enlargement of our sympathies. We start as completely tribal beings, for whom the destruction of the neighbouring tribe is a pure blessing. There is no suggestion that God, or whatever spiritual entities preceded the idea of God, has any objection to the elimination of rivals.
The idea of a fundamentalist atheist seems a contradiction in terms. Fundamentalists, at least since the emergence of the term in the early twentieth century, are people committed to a particular interpretation of a text: at least that’s what they claim to be. Atheism has no sacred text, although there are atheist cults.