Kwisatz Haderach

This isn’t a plot hole. You’ve overlooked one of the most important details in Frank Herbert’s ecological appendix. The Fremen weren’t planning to turn the entire planet into a green paradise overnight. Their terraforming project was designed to happen gradually, over generations. And here’s the detail you missed: Liet-Kynes knew perfectly well that the sandworms were essential to spice production. In fact, he explicitly warned that Shai-Hulud must never be destroyed, otherwise the spice wealth of Arrakis would disappear. The plan involved carefully balancing vegetation, water and the existing ecosystem rather than simply wiping out the desert. The Fremen wanted a planet where their children could live without constantly fighting for survival. They weren’t trying to destroy the very thing that made Arrakis important. Frank Herbert actually put a lot more thought into Arrakis’s ecology than this question gives him credit for.