In Germany after the official surrender there was still occasional trouble from fanatical SS/HY holdouts who fought to the last man and a half-hearted guerilla resistance campaign, the Werwolf movement.
Did occupation troops in Japan after the surrender face any trouble? Did the Japanese have any equivalent to the Werwolfs? Given how ferocious they were it combat it seems strange how servile and cowed they were during occupation (granted two massive bombs and the command of the god-emperor might have something to do with that). All I can find on Google is tales of the holdouts in the Pacific rather than Japan herself.
I think that MacArthur’s grasp of how to properly run an occupation in East Asia also made a big difference. Possibly his greatest accomplishment in life.
Rapes occur pretty much everywhere, and especially in wartime. However, there is no actual evidence that occurred in this case. Further, there is no evidence the 3 Marines killed were even the right people, if repeated assaults were indeed happening.
Considering the Marines were identified by name and location, and there is no criminal investigation being done, blindly labeling them rapists is pretty insulting to them and their likely families.
Being “killed in retaliation for some rapes” is not calling them rapists.
OTOH, it is very likely that they were rapists. Not proven in court or anything, but very likely. I don’t see any reason to defend them in particular.
There were a huge number of rapes in Okinawa at the time. Far more per capita than on the main islands. Which is why when I saw the OP’s question I did a search for incidents on Okinawa, where the tension between the civilians the US military has been extremely tense ever since.
The fact that the three were written off as deserters with little interest in determining their fate does speak volumes about the racism of the era, however.