The most likely consequence that resulted from sacred Indigenous religions being banned by Europeans is the loss of Indigenous religious texts. When Europeans enforced Christianity and suppressed Indigenous beliefs, many sacred texts, oral traditions, and cultural practices were either destroyed or driven underground. This resulted in a significant loss of Indigenous cultural heritage and religious practices.
While some Indigenous myths and histories may have been preserved through oral tradition, the systematic efforts to convert and assimilate Indigenous peoples often led to a significant diminishment of their original religious frameworks and texts. The other options you mention—such as conquistadors immersing themselves in local cultures or Christianity becoming a minor religion in South America—were less likely to be direct consequences of the banning of Indigenous religions.