Actually, while the first book does promote that assumption, all the others don’t so much walk it back as take a wrecking ball to it. But I never read Dune as anything other than a misanthropic dystopian romance written by someone with a profoundly negative view of humanity and religion. If you read the The Jesus Incident or any of the other WorShip books, you get a look at how much Herbert really hated religion. And Whipping Star is basically one long satire of organized anything.
That’s kind of my point though. That’s the fatal conceit. There’s no winning a fight against evolution, artificial or otherwise. We can unpredictably change the direction by throwing wrenches into the works, but as antibiotic resistant bacteria demonstrate, that can backfire as easily as it can work in our favor.