Sir Terry Pratchett's 2008 novel Nation is a fantasy novel set, by the author's own explanation, in an alternate universe, but it serves to highlight and examine many actions, reactions, and motivations in the real world. In this sense, it is absolutely a piece of social commentary on the interaction between Exploration-Age Europeans and native tribes living isolated on islands and shores.
The most obvious example is the delineation between a native tribe's accepted religious structure -- particularly their gods -- and the real world's general focus on pragmatic, working solutions to problems. Throughout the book, Mau, the protagonist, makes his own way in the world and solves his own problems through thought and deliberation, but still finds himself praying and thinking of godly beings as affecting everything in his life.
Are trousermen women the same as real women? he wondered as he ran. She got very angry when I drew that picture. Do they ever take their clothes off? Oh please, please don't let her say no!
And his next thought, as he ran into the low forest, which was alive with birdsong, was: Who did I just say "please" to?
(Pratchett, Nation, Google Books)
Focused on bringing a women to help with a childbirth, he instinctively sends up a minor prayer: "please." But he also questions both the recipient and the meaning of the prayer, and its value vs. his actions. Normally, the prayer would be an almost unconscious part of daily routines, but Mau has had to question his entire life, and finds blind devotion troubling. He constantly refers to "the new world" that he is living in, one where his simple heritage is on shaky ground. While he is not explicitly oppressed or abused by "trousermen," his movement away from his heritage and faith is very much like the European push to convert islanders and native peoples during the Age of Exploration.