If an author wanted to ridicule a religion or a belief without being rude and straightup calling it "stupid," how could he or she do it?

You can simply disagree. For example lets use the Church of the Flying Spaghetti Monster. I dont agree that the climate changes result in hurricanes or earthquakes based off the number of pirates available to hijack cargo ships. I believe on scientific facts that I have been presented with and that can be proven.

She could use euphemism it is a figurative language that is used in place that can suggest something unpleasant but in the kindest way possible.