@clacke I didn't feel that the film was unclear on this. She clearly knew her own mind and we saw several examples of this throughout.
Paul did spring the marriage to Ireland and, with the way Chani's character had been portrayed, it was completely within character for her to leave in the way that she did.
She didn't agree with the direction Paul was taking. She knew she couldn't change it. Leaving was the only option left open to her.