As a libertarian you probably subscribe to the non aggression principle.
Taking another life because it through no fault of it's own found itself in your body is aggression. That person didn't ask to be put there, indeed is only there because of you're actions.
There are plenty of libertarians who absolutely do not believe in abortion.
Presenting the pro-life case to libertarians, and the libertarian case to pro-lifers http://www.l4l.org/index.html