I would look at it differently.
I understand why Japan, an ally of the US, would not want to pursue the case aggressively. The concept of "losing one's face" is not only applicable inside the country. They think that they'll make US lose its face, if the assailant lived at the base, that's why.
IRL, being a (rather) newly minted US citizen, I can tell that it is viewed very differently here. I think i have the mentality of a liberal American, and understand how people here view it. The problem is not whether he was a Japanese, Korean or a US citizen. We women are tired of these killers walking inside the community. We want safety for ourselves, our families and our children. Four people = a SK.
Given where the world is today, I have little concern if it is found out that the person was from a US base. GRK served in the military, Keyes did. No big deal and no shame for the military. Even if he was the son of someone important, in our world, the father does not bear responsibility for the kid. I have a feeling that Japan is a good ally and can bet that it won't be a big issue between the countries, either. In fact, today is the good time to act.
But - I think that if Japan has reason to believe that the perp has left the country, they may ask the Interpol to help. If they believe that he lives in the US, they can collaborate with the US.
Enough of these potential SKs threatening us and our kids. He has to be isolated and on meds.
Also - the sand can help, but not much. DNA = everything.