I always took it as the marine being killed when the Predators showed up to get Lightstepper. There was a "truce" between them at the end of the story sure, but clearly the Predators showed up before the marines did and the banner and final words of the story imply that they killed him when they did.
And even if you take it that they let him live and just took the banner as a trophy, Machiko's still not wrong. They killed several marines before the Predalien showed up even if that last guy wasn't one of them, so her conflicted feelings about being a part of a group that happily kills humans are warranted either way.