(Wearily) "It banned the works of Copernicus and Kepler, and placed Galileo under house arrest."
It (the Church) didn't quite.... Kepler was a Protestant who refused to convert to Catholicism but he was employed and protected by the Catholic Emperor Rudolph II, and offered a post at the University of Padua. Copernicus was in minor orders in the Catholic Church. When his heliocentric theories were relayed to Pope Clement VII the Pope was delighted with him. Copernicus dedicated his masterwork 'De revolutionibus' to Pope Paul III. Only some eighty years later some protests were raised against heliocentrism - they were also raised by Protestants including Luther, Calvin and Melancthon (although his objection seems to have been as much to the fact that Copernicus was Polish as to a belief that he was wrong).
Now. Galileo. The Pope was happy enough with Galileo's theories until he decided to publish them in the form of a dialogue between himself and the Pope, under a name that can be roughly translated as 'Silly Big Thicko'. It was very wrong of the Pope to take offence at this - but understandable. Galileo was condemned to house arrest, but allowed to choose which houses he had to stay in. He was also supposed to repeat the Penitential Psalms every few weeks, but one of his daughters (both nuns) petitioned the Inquisition that she should be allowed to say them for him, and they agreed. Galileo was allowed visitors, including John Milton. His researches were continued at the Vatican Observatory.
As to scientific papers being published in Latin, of course they were. Latin was the lingua franca of the scientific world, not the private language of the Church. Everyone who had any education learned Latin, and the advantages of writing a book in Germany, France or Italy in a language that could be understood by an educated person anywhere in Europe are fairly obvious.
If someone would like to furnish me with a list of 'persecuted and tortured' scientists I would be very happy to see it.
And the church never had a problem with Darwinism. Why would she?
The suggestion that England had better guns and ships than Spain is nonsense. The Armada wasn't out gunned or out-sailed, it was beaten by the weather. The Vatican had a foundry, and and was as expert in making cannon as any other power.