Allowing a rape exception would equally likely encourage false reports of rape.
The issue is a tough one, with no really good answers. The notion that a child should have to suffer for the sins of a parent is hardly unknown in the Bible, and the sin of a rapist should be considered grave indeed. I am unaware of anything biblically that would require that a pregnant adulteress be allowed to live long enough to give birth; killing the adulteress before she bears a child avoids any risk that the child might challenge the legitimate heirs of the woman's husband. Religiously, I thus think there's room for argument. I really don't see any resolution to the problem of false accusations, though.
Children suffer the consequences of their parents evil, but to lay that at the feet of God amounts to blasphemy. God never punishes the innocent for the sins of the guilty (Ezekiel 18). God acts to inhibit the sins of the guilty, and in so acting innocent people are harmed.
It is important to remember that God has the authority to take life, and man does not except in the case of a government exactly capital punishment on the guilty. God often takes the (physical) life of the righteous or innocent, but that is not punishment. In fact, it is a mercy that is reserved to God.
A woman who shoots a rapist is justified. But if she shoots his sister or his child, that is not justified.