I think the "extraordinary implications" for these two soldiers is that it's wrong to beat up an Afghani commander who is supposedly an ally of the US forces. That's not to say that I think the pedophilia practiced by our allies is "okay" or that any of us is willing to ignore it.
Afghani (and Iraqi and others in countries around the world) women and children who report being raped are sometimes re-victimized by the authorities who - we expect - are supposed to be there to protect them. What if the US forces insist on being able to step in regardless of local laws, and our intervention leads to just such an outcome? How is that helpful?
Exactly. There is a good chance of victims being stoned to death for having been abused. Or worse.
Our military is not equipped to undo centuries of practices in foreign countries. It also is not our mission.