Because Alia’s still busy in the womb throughout the movie, it’s Paul, having learned about his true lineage, who has to deliver the killing blow. During the attack on Arrakeen, Paul storms into the room where the Emperor and the Harkonnens are meeting, and he fatally stabs the Baron. “Grandfather,” he says, “You die like an animal.” It’s a cold moment, in part because it doesn’t even seem like the Baron knows he was Paul’s grandfather in the first place. He’s given this groundbreaking bit of information, and then he has about five seconds to make peace with it before the life leaves his eyes. It’s still more time than Alia gave him, because in the books, her Gom Jabbar kills him almost instantly.
Adding more indignity to the Harkonnen’s movie death is the way the Emperor turned on him before Paul stormed in. The Emperor signaled to one of his Sardaukar guards to break the Baron’s flotation device, as well as the breathing tank he was hooked up to. Even if his grandson hadn’t killed him, it doesn’t seem like things were on the up and up for the Baron anyway. In some ways, this makes his death a little more merciful than the book’s version: when book Alia suddenly killed him, the Baron’s political prospects weren’t quite as bleak.
It’s not too surprising that the movie changed up the Baron’s death, as his death scene was nowhere near as memorable as the deaths of Leto or Feyd-Rautha of Jamis. As cool and sudden as Alia’s killing of the Baron was, it was still somewhat anti-climactic for such a built-up character. Book fans don’t have any huge attachment to the way this scene went down, so it’s not a huge deal for Denis Villeneuve to tinker around with it.