I suppose it depends on where you stand on a moral level. The end goal for all life is to reproduce however, or rather, to pass on your genes. In by allowing your rapist to plant his seed and perpetuate his line, you've done him the ultimate satisfaction regardless of his demise. When good man do nothing, evil prevails. Sometimes the hard choice is the right choice, even at the cost of dignity and forsaken lives.
The topic of abortion vs keeping the baby of a rapist is completely controversial but I believe that no one born evil. The mother in this case lost her memories of how the child was conceived and even though we completely acknowledge that it was an irredeemable act committed we can only assume that the mother going forward does not harbor negative thoughts about the origin of her child and will raise him/her as one of her own and along with the father pass on the same teachings their parents gave them that allowed them to grow into proper and responsible adults. Assuming the rapist dies at the end, wouldn't it be a slap in the face of their bloodline to stop the perpetuation of evil that way? If we accept that ending D is the best ending then we can only assume that the protagonists children could become as immoral as their parents