Rodrigues's Japanese interpreter isn't exactly fond of the Catholic Church. Though he's a bit of a jerk about it, it's hard to argue with his opinion after hearing his story.
The interpreter learned how to speak Portuguese at a seminary. It wasn't a great experience: there was priest there who "had nothing but contempt for everything Japanese"—"even those [...] who graduated from the seminary he did not allow to become priests" (5.64). With this as his first interaction with a Western priest, it's understandable that the interpreter would be bitter toward Father Rodrigues and his peers.
But don't let the guy off the hook completely—it's not like he went in with the best of intentions. As he states himself, he "had no wish to be a Christian nor a brother" because he's "the son of a court samurai" (5.62). In other words, he doesn't need any help from the Church to gain power for himself. Though the missionaries may have mistreated their Japanese students, the interpreter—and the Japanese government as a whole—isn't exactly taking the high road, either.
It's all about power, really, and the ironic thing is that while the interpreter complains about the unequal treatment of the Japanese Christians by the Portuguese priests, he himself wants to enforce inequality among the Japanese as a whole.