It is indeed protecting a child. But it is also a violation of free will. In your example we do have free will today. You can plot to blow up a building. No one can stop you from plotting to do that. However, if you're caught, you are punished. I understand that some freedoms can be taken away. In that sense we don't have free will today. Neither do we practice perfect justice. Which is why a child rapist can get away with a six week jail sentence after being convicted.
Free will is either "free" or it is not. If we are not "free" to do whatever we want, we do not have free will.
Nonetheless, your example is still in conflict with point 1. If you stop a rapist from raping, you must also inhibit a person's thoughts when they desire another man's wife (a sin according to the bible).
The only reason we don't stop people from plotting to blow up buildings is because we can't catch them. God could catch them, so why doesn't he?
We're not free to do what we want. We're constricted in every way. We can't fly unaided. We can't expand to 30 times our size. And in civilized societies we can't decide to kill someone and then go do it. We're not "free" to plot murder, so long as we understand we'll get punished for it. We simply can't do it. The only reason some people manage to do it anyway is because our crime prevention isn't good enough to detect the act in progress and stop it. God could, but he doesn't. When our technology allows us to stop people BEFORE they commit crimes, we will. (Oops, anyone thinking "minority report"?)
Your last point is a classic all-or-nothing bit. No, stopping a rapist doesn't in any way require me to also inhibit a person's thoughts. "Boy, I'd like to have sex with her" and actually planning to rape a woman are two very different things. (Regardless of what the Bible may say about it.) God could allow anyone to think anything, and only intervene when their actions impinged on another person's rights. Where do you draw the line? I don't, but then, I'm not God. Presumably, he would know where to draw the line.
His choice (if he exists at all) has been to simply not take any action at all. If he were anyone else, he'd be publicly denounced for such neglect. But he's God, so he gets by with it.