Your theory could be correct.If these Marines are tried in a Philippine court,one can only hope they use DNA tests,and accurate ones at that.
DNA cannot tell whether the sex was consensual or not. Unless the woman is pretty badly beaten, physical evidence that the sex was rape is often pretty thin.
Which, of course, puts it back into the "she said, they said" category, in this case. Although the driver might be a comparatively unbiased witness.
It is even harder to disprove rape than to prove it. Which is, IMHO, a dang good reason to keep your pants zipped.