he definitely did something to help her remember because I'm pretty sure he says something about getting reacquainted, remember MIB is/was a board member he can easily have knowledge about the hosts and their code. Plus raping a host is completely beneath the MIB he remarks about most guests just coming here to get their rocks off by fukking and killing, he's trying to find the maze.
It was a clever filmmaking technique to make you think it was rape due to the first impression we get of the MIB, once we know more about the character you realize (or should) that he didn't just rape her in the barn. A couple of my friends didn't even know about the multiple timelines that we're seeing