Obviously that was the point of the author, but yes it's overthinking it. You can't expect to tell the entire story and multiple complex themes (ecology, politics, the dangers of charismatic figures, etc.) of an 800 page novel into a 2.5 hour film. To successfully adapt an "unadaptable" book and appeal to the lowest common denominator movie-watcher, you need to pick and choose.
In this case, Denis chose the dangers of charismatic/messianic figures as the the central theme of his adaptation. That and the love story between Paul and Chani, the latter of which he gave a bigger role compared to the books. I do agree on some of the author's points and wish the movie included more things from the books, but you can only fit so much into a movie. Hell, they probably could've made just the first book into a trilogy in itself, then Messiah as the fourth and conclusion.