As for your specific examples: no, explanations of the mechanisms behind lightning, rainbows or earthquakes were not very problematic for the church. Mechanical explanations did not discredit God or the bible; it only explained through what physical mechanism God made these things possible. Theologians would never reject mechanical explanations - because they were perfectly happy to admit that God's acting in the world is often done through mechanisms.

There are a few exceptions to this general rule, such as Darwin's theory of evolution. Though it was merely a mechanism for speciation and adaptation, it was very harmful to religion, because it provided an atheist alternative to the argument from design. Before Darwin, the biological argument from design had been central in Britain's fight against atheism, as no atheist could give a feasible explanation for the design apparent in animals. Likewise, 19th century geology created quite some controversies by showing that the earth was millions of years old, and that landscapes developed gradually instead of through great catastrophic events such as Noah's flood.

As a larger point: despite how it might look from certain events (such as Galileo's trial), religion and science were usually not enemies. Newton was considered a very pious Christian, and his work was praised by British theologians because it proved God's divine presence in the world. On the continent, the struggle between science and religion was a bit more evident, but still most of the time it was a pretty decent alliance.