>>213590195 (OP)
They knew the Harkonnen were up to something, what many fail to notice (though it's said in the film multiple times) is that this operation was so insanely expensive that the Harkonnen were basically broke by the time they got Dune back.
The Harkonnen were only a Barony, a relatively minor family compared to the Atreides, they had to leverage so much of their wealth and power just to get Dune back that the only way they were able to remain solvent was by squeezing the planet to an insane degree, brutalizing the locals, extracting as much Spice as possible and trading everything--lives, public goodwill, peace--to expedite it.
The ultimate failure of the Harkonnen wasn't even them being evil, it was that they were simply unaware that the Fremen population was large enough that it could actually threaten Imperial hold on the world by rising up. They thought there were a few thousand of them, not millions.
Personally I always felt this was actually undermined by the Fremen being these super-soldier types, which really made no sense. Desert people aren't good at fighting, they're good at surviving.