Yes, it's her choice. And that's why, if it's the wrong choice, she can sometimes be considered guilty. I say "sometimes" because you can sometimes commit a wrongful act without being morally guilty, if there are enough extenuating circumstances. But even in this case, the act itself remains wrongful.
And the fact that a person suffers doesn't give that person the right to commit a wrongful act, even if it's in order to stop the suffering. So although the woman impregnated by a rapist may suffer a lot because of that pregnancy, it doesn't give her the right to murder the little human she's carrying. The fact that this would be legal doesn't mean it would be moral.