I am not sure if you are asking about “gold and silver” or “God and silver.” I will assume that you are asking about God and silver. If you are actually asking about gold, no harm done, because the answer for gold is the same as the answer for silver. Both God and silver increased the Europeans’ desire to dominate the New World, thus making the Columbian Exchange more intense and more harmful to the natives of the Americas.
When the Europeans discovered silver (and gold) in the Americas, they became more motivated to explore and to dominate the region. This meant that more Europeans came to the Americas, bringing more of their technology, horses, germs, and cultural practices. As they spread out across the continents, their presence became more and more overwhelming, submerging or even destroying native cultures.
God (or, more accurately, religion) also intensified the Columbian Exchange. Many Europeans felt that God wanted them to dominate the natives, in part so they could convert those natives to Christianity. As with the silver and gold, the desire to evangelize caused Europeans to spread out across Latin America, bringing them in greater contact with more natives and helping to spread European ways. In particular, the desire to convert the natives led Europeans to impose their own religion, thus weakening native cultures.
In these ways, both precious metals like gold and silver and the desire to (as they saw it) please God led the Europeans to dominate the New World more thoroughly, intensifying the Columbian Exchange and changing the lives of natives more radically.