Don't blame it on the Navy. Blame it on black enlisted personnel. Japan even petitioned to have the US military stay in Japan IF they excluded blacks. I think their version of SECDEF publicly said that he had no problems with Americans, just crimes committed by American blacks in the 90s.
Is Japan a racist country? No. However they have a VERY low level of tolerance for inappropriate behavior and violations of normal, polite, formal social etiquette.
The rapist is white this time so I guess some modern adjustment can be made. With the rising (or just being reported) rape rate in the military as a whole (male vs male, too) I think it is a symptom of our whole nation sliding into the immoral abyss that has been going on for decades.
When God dies there is no fear of consequences.