If you made the Fremen, BG, and Sardaukar into base classes, they won't be balanced. Fremen and the BG are better warriors than the Sardaukar, who are better still than even House Atreidies and Harkonnen warriors.
You are dealing with more than one race in DUNE. Remeber the Face Dancers, and Guild Navigators. Anyways, it fits with the "breeding" theme of the setting to make different peoples into different races.
Hmm... maybe that's the best way to do it. The Fremen, Sardaukar, BG, Mentats, Face Dancers - they are all templates or races that you can add to the base classes. (They are all are raised from birth, I think.) The Kwisatz Haderach could be another template.
The "wierding way" should probably be represented by skills and feats, not typical D&D psionic powers.
Hmm... I still think that most "base" classes should be prestige classes, with entry requirements such as "born on Arrakis and raised as a Fremen", or "born on Salusa Secundus", or whatever.