The eugenics program was absolutely 100% intended to wipe out entire groups of people. What makes this so fascinating to me in Dune is it asks the question:
“If you knew (by literally seeing the future) that humanity was doomed to its own extinction, and tens of thousands of years of eugenics, austerity and technological dark ages could save the human race, would you choose that path?”
The question creates some unbelievable moral quandaries backed against something that could only exist in sci-fi - knowing the outcome for certain. It’s part of why I love the genre so much - you can discuss hypotheticals that literally cannot exist in reality.