I disagree, Terminus.
DUNE is not nothing more than an ecology book. If it was, it wouldn't go deep into discussions on the combinations and manipulations of religion; the limitations of the superhero; the faults of political leaders; and the science of drug addiction, water preservation, space travel, mind consciousness, and time perception.
I know that Lem hates the idea discussing or approaching the idea's of another writer's work (especially if the work is below his standards for excellence), but, hypothetically, if Lem had handled aspects of DUNE himself, I suspect that he would try to be more scientific about the life cycle of the sandworms, the elemental composition of the spice, the unforeseen dangers of prolonged spice addiction or reliance, and the nature of Paul Atreides' oracular visions. Lem would also have explained the science of robotics in DUNE, how machines were able to think like humans in DUNE, and how scientists were able to dumb down machines so that another Holy War Against Thinking Machines would no longer be necessary.
Frank Herbert was more interested in how leaders manipulate situations to suit their own ends, and how the mistakes of authority figures and heroes are amplified by their followers. He also believed that superheroes would be even worse than regular heroes, because their mistakes are even more catastrophic.
If Stanislaw Lem wouldn't have liked the book, it could be because Frank Herbert doesn't appear to be critical of the hero figure for playing god and choosing the most destructive path for the future. It could also be because he would regard it as more science fantasy than science fact, and the reliance of adventure to progress the story. The exception with Herbert's adventure is that he relies more on complex characterization and psychological sophistication rather than on adventure alone.
Perhaps the deeper complexity of the book would be better perceived through a masterful Polish translation, with a Polish equivalent of Michael Kandel.
I rather see Lem as possibly being like a Guild Navigator, because Lem sees into the faults of human civilization the decisions it makes. Lem also has the ability to steer human thinking in a direction likened to a Navigator: he sees through all the complexities, and folds them to safer course. In the DUNE appendix, they have this to say about the Guild and other higher authorities on the nature of religion and human behavior:
"Any comparison of the religious beliefs dominant in the Imperium up to the time of Mua'Dib must start with the major forces which shaped those beliefs...
3. The agnostic ruling class (including the Guild) for whom religion was a kind of puppet show to amuse the populace and keep it docile, and who believed essentially that all phenomena-- even religious phenomena-- could be reduced to mechanical explanations."
Somehow, I sense the cyberneticists of THE CYBERIAD and a bit of Lem in the Spacing Guild (Except for the religious manipulation part). Lem would have attributed a lot of satirical/scientific commentary on the Guild (if he was alive and interested), but that wouldn't be something Lem would want to do.