In Dune, Paul uses his ability to destroy the Spice (with the Water of Death) as leverage to force Shaddam IV to give him the imperium. However, doesn't this unique position give him the power to violate the Great Convention? None of the Great Houses would use their atomics to destroy Dune, because that would destroy the Spice. That means that as long as he is on Dune, Paul can use the Atreides house atomics with impunity without fear of retaliation. Since Paul controls the Fremen on Arrakis, he should be safe from invasion as well. Why does Paul risk hand-to-hand combat when he could take the imperium from the safety of Sietch Tabr? If it was due to the Atreides moral code, why didn't the Harkonnens try it when they controlled Arrakis?
In point of fact, Paul Atreides does use the family atomics, for the short-term goal of taking over Arrakis from the Harkonnens, and the Empire from the Emperor.
"My Duke", Guerney said, "my chief worry is the atomics. If you use them to blast a hole in the Shield Wall..."
"Those people up there won't use atomics against us," Paul said. "They don't dare...and for the same reason they cannot risk our destroying of the spice."
But the injunction against--"
"The injunction!" Paul barked. "It's fear, not the injunction that keeps the Houses from hurling atomics against each other. The language of the Great Convention is clear enough: 'Use of atomics against humans shall be cause for planetary obliteration.' We're going to blast the Shield Wall, not humans."
The Houses and the Spacing Guild are in no position to retaliate. Presumably, "Planetary obliteration" would have destroyed the spice as much as the Water of Death.
There is an "injunction" against the use of atomics, but Paul is justifying their use as military engineering, not as a way to kill his enemies directly. He gives the Houses and the Guild an out this way.
"It's too fine a point," Gurney said.
"The hair-splitters up there will welcome any point," Paul said. "Let's talk no more about it."
It's clear that the atomics are actually used from this scene with the Emperor:
The Emperor surged to his feet. "This play has gone on long enough. I will take your brother and this planet and grind them to--"
The room rumbled and shook around them. There came a sudden cascade of sand behind the throne where the hutment was coupled to the Emperor's ship. The abrupt flickering of skin pressure told of a wide-area shield being created.
"I told you," Alia said. "My brother comes."