In real life, Lois would probably be considering the A-word. Being pregnant with a rapist's child is definitely one of the more accepted reasons that a woman chooses that route.
Since I doubt that Lois would opt for that, I think that Clark would offer to marry her and make a family out of the situation. You didn't say if the rapist was a different race or culture, and of course, if that was the case, they wouldn't be able to have people think that Clark was the father.
You've definitely got some different routes to go here with the story. I await!
