Well there you go, fetus mother relationship is unique so you can't just apply regular laws to it. But even if you did you still need to prove to court or government that your action in self defense were justified or you will get charged with a crime.

Any time you take a life, even in self defense, there is an investigation process that determines if state has a right to lay charges. If you have a good case then you go home, but if not and something in your self defense story does not check out, you go to jail. SO yes the government or court has a say in what you do to others even if it was your body and it was self defense.

There is literally cases all over the world, US included, where rapist, attacker or intruder get killed by the victim and the victim goes to jail.