Is preparing bonus payrolls, determined by the manager based on his personal discretion and tainted by favoritism, considered a sin necessitating leaving the job, especially since there is another alternative in the company that requires participation in procedures related to usurious loans and pension insurance?

As long as the awarding of bonuses is left to the manager's discretion and trustworthiness, he is responsible. Mere suspicion about his favoritism does not prevent you from preparing the reports and staying at work. You can advise the manager to fear Allah and observe trustworthiness, for what he gives is not from his private money, and he is accountable for what he spends unlawfully. Indeed, "the religion is sincere advice" for Allah, His Book, His Messenger, the leaders of the Muslims, and their common folk.