How did the religion of paganism turn from the worshipping of Mother Nature to the worshipping of witchcraft?

Paganism did not turn from worshiping nature to witchcraft; this is a confusion between paganism as a spiritual belief and witchcraft, or magick, as a practice.

Paganism encompasses many religions; what they all have in common is that they're all non-abrahamic in origin (they're not descended from Judaism, Christianity, or Islam). Wicca, Ásatrú, Hellenic Polytheism, Buddhism, the Native American religions, Taoism, and Shinto are all examples of pagan religions. Not all Pagan religions are nature based. Some are based on human concepts such as valor, civilization, arts, and economics.

The very phrasing of this question is ludicrous. One can practice witchcraft, but one worships some form of divinity.