I would agree with your assesment except for one thing:
"Smith and the others, along with the woman, had been drinking at a bar and were rushing back to the USS Essex to beat a curfew, he said."
Why would the woman be going back to the boat if she was a bargirl. Notice there is no mention of the girl's nationality.
I'm thinking there's more to the story.
Why would the Philippines be upset over Marines raping a woman if she wasn't one of theirs?
"Why would the woman be going back to the boat if she was a bargirl."
In that town, you "check out" your girl for the night. You pay the "bar fine" and she is free to go with you all night.
Not that I've ever done it, and not that there's anything wrong with it, but haven't you ever bought a bargirl out of a bar in the far east?