It does appear that any incest between Paul and his mother is all in Lynch's mind.
However, on the subject of incest in Dune:
From another source, related to a the influence of Herbert on Star Wars.
Herbert borrowed several other riffs from Sophocles, including the blind prophet, the hero becoming blind at the death of his wife, and the flawed person being sent out into the wasteland to die (rather than burdening his family and tribe). Herbert also flirted with the subtheme of incest: if love can only exist between equals, there aren't enough superhumans on Arrakis to go around, so Atreides siblings tend to fall in love: Leto II and Ghani follow the Path of Light, refusing to act on their almost romantic love for each other. Alia is in love with Paul, so she arranges for him to chance upon her when she has no clothes on. This attempt to seduce Paul into an incestuous relationship is evidence that Alia has fallen to the Dark Path.
The linked site is an interesting read on the similarity of Star Wars and Dune and the influence of Shakespeare and Sophocles et al on Herbert. It also speculates on who the characters represent in the writer's (the essay not Herbert) opinion, I suppose. Harkonnan, the Turks, The Imperium, England and the Germans, more if you care to read it.