We find a good example of lack of respect for other people's religion in "Secret of Hondorica" (DD 46-02). Donald goes to Hondorica with his nephews to find a missing letter. So does Galdstone Gander. He is captured by the natives in the area because they hate helicopters. Helicopters look like their evil god Bru. Donald looks like the native's god of good eating (Chu), and the ducks use this to free Gladstone - Donald (and later Gladstone) tries to convince the natives that he really is their god.

A similar episode occurs in "Land of the Totem poles" (OS 263-02). Donald wants to punish some naives who do not understand how to use the produckts Donald sells. Huey, Dewey and Louie uses the totempoles in the village to play the organ and scares the villagers out of their wits. When they realise what has happened, the natives buys 400 steam organs.
It is a bit better when Donald fools Scrooge in "In Kakimaw country" (WDC 202-01) by dressing as a medisin man and invoke Manitou and Thunderface pretending to make the rain fall. Donald is not punished for his trickery, and gets his vacation while Scrooge gets the rain his been waiting for.
A bit different is Gnasty Face in "Mystery of the Swamp" (OS 62-03). A big temple is built to worship him, but he never helps his people.

Several times the ducks go to South and Central Amerika. We see Indians (of the native American kind) sacrificing gold to their gods in two stories - Bark's "The Crown of the Mayas" (US 44-01) and Don Rosa's "The Last Lords of El Dorado" (D 96066). In "The Crown of the Mayas" we get the explanation for the sacrifices - they are made to appeace the gods.
A bit different is "The Son of the Sun" (AR 102). We are told that the descendants of the Incas wait for the Son of the Sun (Manco Capac) to return.They believe he will save them (yes, there are parallels to Messiah in the old testament). The prophesy about Manco Capac's rerurn is, in a way, fulfilled as his temple falls into the lake they are living by when Scrooge and Flintheart Glomgold makes a volcano erupt.

In "The Lost Charts of Columbus" (D 94144) the ducks pay the aztec city Teotihuacan a visit. We can see a sculpture representing Quetzacoatl's spirit in the city.