Futuristic Theocracry?

Dune is a science fiction novel which takes place in a universe full of 'space ships', multiple inhabited planets, and strict rule by one family. Because the reader experiences the past novels from the 'kings' point of view, we don't really notice the harsh realities and barbarianism going on. However, in the third novel in the dune series, Frank Herbert really steps up the nitty gritty, and begins to make the reader frown upon the theocracy which has been set up.

"Javid came hurrying to report that Paymon had been over-heard to mutter the fateful lines from the Orange Catholic Bible ..... In a flush of ragesuch as she'd never before experienced, she ordered Paymon's immediate execution, sending his body to the Temple deathstill where his water, at least, would be of some value in the priestly coffers." (Herbert 58)

I think the author is trying to express his views and questions of the world through this Theocracy. I believe he is trying to ask something along the lines of 'Even hundreds of years from now, will religion prevail over technology, over common sense? Will war still be waged over resources rather than shared? Will our leaders always be corrupt to some point, or will they eventually become wholesome and selfless?'.