Here are a couple of quotes from Beyond Good and Evil:
As far as materialistic atomism goes: this is one of the most well-refuted things in existence. In Europe these days, nobody in the scholarly community is likely to be so unscholarly as to attach any real significance to it, except as a handy household tool (that is, as an abbreviated figure of speech). For this, we can thank that Pole, Boscovich, who, together with the Pole, Copernicus, was the greatest, most successful opponent of the visual evidence.
... Boscovich taught us to renounce belief in the last bit of earth that did "stand still," the belief in "matter," in the "material," in the residual piece of earth and clump of an atom...
Wikipedia states that Boscovich "produced a precursor of atomic theory." This seems to contradict the achievements that Nietzsche is attributing to him. I don't understand why Nietzsche would be claiming that atomism is "well-refuted," or why he would claim that one of the forefathers of atomic theory had helped to refute it.
At first, I assumed that Nietzsche must be using the word "atomism" in a way with which I am unfamiliar. Then I read on to this quote:
... we must also put an end to that other and more disastrous atomism, the one Christianity has taught best and longest, the atomism of the soul. Let this expression signify the belief that the soul is something indestructible, eternal, indivisible, that it is a monad, an atomon: this belief must be thrown out of science!
Here, Nietzsche defines what he means by "atomism," and it's exactly what I imagine when I hear the word. It seems as if Nietzsche is asserting that it is obvious that the universe and all matter is continuous (not discrete). Was this really the consensus at the time?