there's a difference between a story with a message, and a message with a story wrapped around it. Monoke Hime has a strong ecological message, but it stands on its own merits. Happy Feet, on the other hand, is a story designed to tell a message.
Dune has a rich political and religious story besides the ecological message, I would be very disapointed if the film makers ignored or truncated those ideas in order to highlight the environmental message.
I would actually like to see Dune broken up into three seperate movies. The first movie would be more politically focused on the intrigues of the Great Houses and ending with the fall of House Artredies and with Paul and Jessica being accepted into the Fremens. The second movie could deal more with the religious themes and end with Paul taking the Water of Life and slipping into a coma. And the third movie would be a big, battle crazy culmination with the fall of House Harkonnen. I really think the book is just way too big and has too many diverse themes to really fit comfortably into a single 2 hour movie.