The villain had evil intentions to kill the merchant and then take their treasures. The Bodhisattva used the method of great compassion to not only prevent the villain from committing the karma of killing, causing him to avoid the suffering of countless kalpas in hell, but also kept the other merchants who had taken the Bodhisattva vows safe and sound. Thus the Bodhisattva figured out a way to kill the villain! The Bodhisattva was willing to endure the fruition of suffering in hell for hundreds of thousands of kalpas due to the cause of killing.
~ With reference to the story of Shanyu and the Five Hundred Merchants in the Upaya-kaushalya Sutra.