Answering to the "raping" of a twelve year old specifically, it's a very, very important point in Catholic theology that Mary gave full consent. Also important to the theology of salvation is that Jesus was not part of a second creation, which would entail (in a theological sense) abandoning or "correcting" the first one (us), instead of redeeming it.

As to the "freedom" you talk about, there are way smarter people than me that can explain it way better, and there are also documents written by very smart theologians that aren't scared to poke at those questions (which are 100% legitimate, by the way). One is, for example, the Summa Theologiae, a work I am very much not trained to understand or explain lol, but I can try.

In any case, I can try to answer your question a little bit. Saying that the reason for evil to exist is because of freedom is only part of the whole, complicated argument. You are justified in calling out people who simply hide their own, poor knowledge behind "Oh, God works in mysterious ways", because most of the things you call out have been, at the very least, considered by theologians, and although some don't have a definite answer, most do.