As the Bene Gesserit taught for centuries, long before they ran afoul of the Fremen: "When religion and politics ride the same cart, when that cart is driven by a living holy man (baraka), nothing can stand in their path."
Appendix III: Report on Bene Gesserit. Motives and Purposes
Because the Bene Gesserit operated for centuries behind the blind of a semi-mystic school while carrying on their selective breeding program among humans, we tend to award them with more status than they appear to deserve. Analysis of their "trial of fact" on the Arrakis Affair betrays the school's profound ignorance of its own role.
It may be argued that the Bene Gesserit could examine only such facts as were available to them and had no direct access to the person of the Prophet Muad'Dib. But the school had surmounted greater obstacles and its error here goes deeper.
The Bene Gesserit program had as its target the breeding of a person they labeled "Kwisatz Haderach," a term signifying "one who can be many places at once." In simpler terms, what they sought was a human with mental powers permitting him to understand and use higher order dimensions.
They were breeding for a super-Mentat, a human computer with some of the prescient abilities found in Guild navigators. Now, attend these facts carefully:
Muad'Dib, born Paul Atreides, was the son of the Duke Leto, a man whose bloodline had been watched carefully for more than a thousand years. The Prophet's mother, Lady Jessica, was a natural daughter of the Baron Vladimir Harkonnen and carried gene-markers whose supreme importance to the breeding program was known for almost two thousand years. She was a Bene Gesserit bred and trained, and
The Lady Jessica was ordered to produce an Atreides daughter. The plan was to inbreed this daughter with Feyd-Rautha Harkonnen, a nephew of the Baron Vladimir, with the high probability of a Kwisatz Haderach from that union. Instead, for reasons she confesses have never been completely clear to her, the concubine Lady Jessica defied her orders and bore a son.
This alone should have alerted the Bene Gesserit to the possibility that a wild variable had entered their scheme. But there were other far more important indications that they virtually ignored: