The war for Arrakis is the classic tale of a small number of colonizers against a larger, motivated, native population. The Harrkonens drastically underestimate the total number of Fremen, and try to fight stand-up battles while the Fremen simply ambush less protected targets. I thought this came across fine in the movie.

The more problematic undertone come directly from Frank Herbert, who had this theory that military prowess only comes from hardship (that's why the Sardaukar are so tough - because the prison planet they are trained on is so harsh), and the Fremen are nigh-invincible fighters because Arrakis is so hard to survive on. This is a misconception that repeats across earlier anthropological study (e.g. ancient Sparta) and is closely tied to the 'Noble Savage' trope.

Also, there never was a fight against the 'resources of the entire empire', Paul and the Fremen fought and defeated the Harkonnens in months-long (movie) or years-long (book) guerilla campaign aimed at lowering spice production. Eventually the Emperor brought his personal forces planetside to restore order. Detachments from the other houses remained in orbit and were not permitted to make planetfall. This is when the Fremen play their trump card of surprise worm attack.