The priest may not be as bad as the doctor, but he’s pretty close. He seems to have as little regard for the natives, and his only potentially redeeming factor is be that he doesn’t physically harm anyone in his pursuit of the pearl’s wealth. His attempt to flatter Kino and Juana is absurdly transparent and only mildly mitigated by the fact that he wants the money for his organization (the church) and not for personal gain.
But the kicker comes in Kino’s later conversation with Juan Tomás, when we learn that the priest has used religion as a tool of oppression against the natives of La Paz. His yearly sermon declares that "each man must remain faithful to his post and must not go running about, else the castle is in danger from the assaults of Hell." In other words: Stay in your place. Don’t challenge the system of colonial oppression, and don’t try to better your lives – otherwise you’ll go to Hell. Low blow, isn’t it?