I also really enjoyed this movie, once I got over the fact that there was no dialog. Yes, the actress did a great job of relaying her emotions throughout.
In answer to your question, yes, the aliens were definitely real and took over the earth by the end of the film. They spared her because they looked into her mind and saw that she killed another human, which was OK by them. In the end, she went from outcast to belle of the ball. The aliens obviously communicated to everyone they took over to leave her alone, she's special.
That's the reason the director gave, that they saw she killed a human so decided to spare her. You can look it up. I never said the aliens killed humans!
You know, that was originally what I thought. I thought they felt sorry for her because of all she endured but then I read what the director said and he said it was because she killed a human, not because they felt sorry for her. It's possible he stated different reasons depending on what interview he gave. I also read that he said it's open as to whether or not it actually happened or whether it was all in her mind. I thought it was very strange that the director of the film was actually saying that. He should know whether his own film was supposed to be reality or not. He sounded really weird!