First, rape is not just an act of violence. It is a violation of free will.
Secondly, from what Jim has shown us, the skinwalker is not the type to commit to a long term plot. I don't think it would pretend to be a loving, caring mate for nine months just for one pay-off at the end. It seems more likely to commit one act that would continue to torture the woman, making her fear what was growing inside her.
After giving birth she could do many different things (kill the baby, abandon it, etc...), but while still pregnant her options would be fewer.
Unless the creature's plan was to create an offspring.