Couple corrections:The Harkonnens thought there were only 50 thousand of them .....when there are actually MILLIONS of them - it was explained in the first movie and this one too.The Freeman just want to left alone but the Harkonnens keep fukking with then ( theHarkonnens believe in just dominating anyone they come across )
Plus they are THE best most savage fighters ...Duncan Idaho a Master fighter was an Atraides ( who were already the best fighters in the Galaxy) and he said he had a hardest fight of his life with just a one on one with a single Freeman
The Harkonnens just have money and fodder ( lots of soldiers ) - thier dudes aren't built like that tho which is why the Baron hires a battalion of Sadukar who are the only ones maybe better than the Atraides
The Sardaukar are the best fighters in the universe (marginally better than the Fremen) until Paul & Jessica come down and give them training. Afterwards, they're able to best the Sardaukar even with a 1:3 disadvantage.
The emperor freely sent his Sardaukar to help the Baron because he got word that House Atreides were training the Fremen, which is a big no-no because the Atreides already had the 2nd best army in the empire by a mile.
Think about it. Another house that is under your rule enlists tens of thousands of troops that are already near-peers to your seemingly unbeatable army. You'd freak the fukk out and try to wipe that house off the map.
I will say this; the emperor should've just wed Irulan to Paul and called it a day. That was the most logical move.