You are missing some very important details. (BTW you seem to know of only one r***/murder, the more recent one, but there were two cases in last few months)
1. fine no people on Earth are happy about foreigner/other race raping and murdering their women, but the reason it's such a BIG DEAL isn't nationality or color. It's that (1) criminal will get almost no punishment due to the extraterritorial rights granted by the allies defense treaty, (2) these crimes happen very frequently, exactly because these soldiers and army contractors know they can get away with, literally, murder, (3) these soldiers are in Japan not to have fun and whatnot, they are there to protect Japan. Something's pretty fucked up if the total number of Japanese citizens killed by American soldiers is higher than killed by the enemies (North Korea, China etc).
2. there are at least 10 times more foreign tourists in Japan than US soldiers, but there's never (big) trouble with the foreigners. Sure some foreigners commit crimes or get in troubles, I would even say, if you dig into the small news stories, a black tourist raping a Japanese girl probably happened a few times already, only never showing up in English news media. Because it's just a criminal case, local news. The police catch the guy, throw him in prison, perhaps the woman is compensated with some money. End of story. No protest, no international crisis. Anyway because tourists know the police can catch them and punish the crime, it doesn't happen much. The Okinawa issue is a big deal because it happens frequently and unpunished.
3. it's a big deal but also NOT a big deal because of the other race angle: Okinawans aren't "real" Japanese. The bases are supposed to protect Japan but strangely located closer to Taiwan, Shanghai and Seoul than to Tokyo. Okinawa is actually often nicknamed "The South Nation", referring to it's historic nationhood before 1868. Okinawa to Japan is similar to Guam to USA, part of USA but not exactly. So all the loud protest and BIG DEAL mainly come out of Okinawan population not the general "proper" Japanese population. So the AV customers, I think, isn't too affected by some almost-Japanese woman being r***ing by black foreigners.
4. it's well known fact that a (white) foreigner only has to learn some minimal Japanese and be not a total jerkass to get free sex with Japanese girls pretty much nonstop. So xenophobia doesn't make (white) on Japanese sex less easy or acceptable. Of course it's very curious IR is almost 100% and it's well reported that a black person has much more difficult time finding free sex in Japan compared to whites. Just one angle to say whatever happens in real world doesn't map 1-to-1 to AV market.