I actually know where you're coming from. They didn't really make it obvious in earlier versions of this story, but the Emperor basically feared losing his throne, and was not an honorable or likeable man.
See, Duke Leto Atreides had become popular among the Landsraad, the main faction of all the noble/royal houses across worlds, partially due to being a good leader, and partially due to having a very well-disciplined army, one that could almost rival the Emperor's Saardukaar soldiers. In the 2000 miniseries, the Baron was having a conversation with his nephews about it, saying that "A popular man arouses jealousy, and the Emperor is a very jealous man." Obviously, Emperor Shaddam IV was not as popular as Duke Leto, and feared that at one point, the Landsraad might vote to remove him from the throne and put Duke Leto there instead, and House Corrino had ruled from that position for centuries.
So he took advantage of the rivalry between House Harkonnen and House Atreides to make his move to get rid of the Duke and everything he had. He made it look like he had chosen House Atreides to take over Spice operations on Arakkis over the Harkonnen, claiming the Atreides could do the job better and more responsibly than their rival. In truth, the Emperor didn't really care about how the Harkonnen treated the people of Dune or how they got the Spice, so long as he got his cut of the profits. He aided House Harkonnen by providing his own Saardukaar soldiers (originally they were disguised as Harkonnen soldiers, but in this film they weren't disguised at all) and other resources to make it look like House Harkonnen had destroyed House Atreides and succeeded.
It's kind of ironic that despite the Emperor's efforts at maintaining his throne, he still lost it two years later to an Atreides, just not Duke Leto.
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