In your example: I don't think this is saying that it's permissible to rape a child. Rather, it's discussing the status of girl who has been raped.
I don't know much about ancient Israel, but I've read that in Iran, if a girl is raped and her rapist is caught, her rapist will be forced to marry her. The marriage is just a formality (just signing some papers at the police office), and will be immediately followed by a divorce. The idea is that the girl's marriage prospects will be better as a divorcée than as an unmarried non-virgin (yeah yeah, patriarchy, I know), and if the girl has fallen pregnant, the baby will have the benefit of not being a bastard.
This sounds similar to me. According to what another poster linked to (before his comment was deleted), the Talmud says that a girl under the age of three who is raped will still be considered a virgin, but a girl over the age of three who is raped won't be considered a virgin anymore. I suspect that might be because they're confident that a girl under the age of three won't fall pregnant, but aren't so confident about a girl over the age of three.
It seems that these rules you've quoted have the purpose of declaring that such a victim (over the age of 3) will automatically have the status of being married to her rapist, and regardless of whether that's a good thing or not, I don't think those rules are necessarily stating that it's "permissible" to rape such a girl.
Contrast that with people who still believe rape, lying, murdering and butchering Jews is fine. I think the disingenuity of your comments are hereby laid bare.