If this was truly a condemnation of pedophilia then why is it limited to male children?

I think the verse in Deut you quoted explains it nicely. A female was just another man's property and as long as they aren't married "rape" was just claiming them. If the women was married both were put to death.

In the end I don't put much stock in this just being a mistranslation as the precedent seems to be homosexuality was sinful, but the argument did have a little more logic behind it than I thought it would when I first read the headline.