Ah the classic, "you don't know what this, so you're dumb, but I'm not going to tell you what it is!" rhetorical move. Very nice. According to this
, materialism is just that there is no magic "soul" or "spirit" and everything is simply composed of matter and energy. This seems to be in line with general scientific thought: science doesn't need to account for something that isn't observably there.
Philosophy of science classes just teach the ideas behind the scientific method, how it came to be, and how the early scientists worked. I don't see what relevance that class has to anything you're talking about, this is not a philosophy that scientists are pushing on people, it is the history of scientific pursuit and tools to be used for future work. There is no agenda, scientists aren't trying to push the ideology on you. The evidence says that is what happened, so they report it. Because you feel persecuted by it because it doesn't jive with your beliefs doesn't make it wrong. It doesn't make it right either, it is simply the best idea we have given the evidence presented thus far. That is all science is.
Your last paragraph is nonsensical. Why do we have to give up quantum mechanics? There is nothing magical about it. It may not even be how things work, it just makes very good predictions. What argument are we following to its logical conclusion? You are simply making statements without fully explaining them. What do atheists have to reject about quantum mechanics?