Actually Darwin was religious (not as much as that many, though) -- which is part of the reason it took him 20 years to publish his ideas.
Galileo, meanwhile, was challenging the established authority but got into trouble more for being rude about the Church than for publishing Scientific ideas. Calling the established authority "simple" doesn't go down well, whether you are right or not.
Like any organisation that has been around for ages, the Church became corrupted and is guilty of many sins, past and present. In the past the Crusades spring to mind, in the present child abuse among others. But equally religion has been a force for good. Many charities were established by the religious (Christian Aid, Water for Life, Barnardo's, etc.).
It's too complicated to say that the Church is wholly good, or wholly evil. FOr better and for worse it has influenced many things. Our Science, our Culture, our Calendar, our laws. Gradually, and rightly in the case of the law in particular, religion is being squeezed out of modern life. To pretend that it hasn't had benefits is to misread history. To pretend, equally, that the thing to do to solve the World's problems is to remove religion is pretty similar. Most of the major religious conflicts are often superposed on deeper poltiical problems -- in Ireland the Catholics v. Protestants problem arrived some 400 years after trouble first broke out; in the Crusades the first victims of the Christian soldiers were other Christians in Eastern Europe; and before many major religions were even thought of it's still possible to find examples of massacres motivated by want of land, money and power.
The biggest evil the world faces is never going to be religion, but Tribalism. Religion is just one manifestation of this scourge, this mentality of "them and us" that is ultimately the main cause of evil in the world. To blame religions is to miss this point.