My two pennies worth on this:

In 1978, Marlon Brando had a small but significant role in Superman, and that helped sell the film. In 1992, Jack Nicholson dominated A Few Good Men, despite only appearing in three scenes. My point: If - and it's a pretty damn big if (I've read the novel and Chani is barely in the first half) - Zendaya's role is well-written enough to make an impact on the film, it won't matter that she's in only a couple of scenes. I think Dune is facing far bigger challenges in addition to those you touched on here regarding the idiotic decision to simultaneously release in HBO, and Zendaya is not the primary draw (although I completely agree she is a great actress and deserves a lead role elsewhere).