Frank Herbert is tapping directly into the vein of Greek Tragedy "which relies on the premise that the universe is deterministic. Fate is hard-wired, and tragedy arises (1) when a hero (e.g., Oedipus) tries to resist his fate although to do so is hopeless or (2) when a hero (e.g., Agamemnon) simply accepts his fate even if it makes him feel icky; either way, the guy is doomed in advance." Gretchen Sween
The Bene Geserit had failed to understand that in achieving a perfect prophet that they would create just such a deterministic universe. This is related to the philosophical free will problem.
It is not too much of a spoiler to say that what the prophet(s) could see were two unpalatable alternatives; one for the human race and one for the prophet(s). The next 3 books explore both the Oedipean and Agamemnon solutions. IMO these three are better by far then books 5 and 6 or the prequels but not the equal of the original.