Is it obligatory for a girl to leave her job at a cargo transport company if prohibited items were found in one of its trucks, given her knowledge that the company owner is helping the detained driver?

There appears to be no impediment to working for the aforementioned company. The sin of its owner will not be counted against you as long as you do not assist in facilitating forbidden acts. The important thing is that you perform your permissible work without aiding anything unlawful, and that you fulfill your religious duty of enjoining good and forbidding evil by documenting these violations and reporting them. Infatuation with a job becomes apparent when you prioritize it over a religious obligation or contribute through it to an unlawful act.