While, I believe now that our moral intuitions come from our evolutionary development, when I was an evangelical Christian, I would have argued that they come from being made in the image of God. Evangelicals themselves teach that they do. Paul taught that they do in Romans 2:14-15:
Indeed, when Gentiles, who do not have the law, do by nature things required by the law, they are a law for themselves, even though they do not have the law, since they show that the requirements of the law are written on their hearts (emphasis added), their consciences also bearing witness, and their thoughts now accusing, now even defending them (NIV).
Paul is making this argument because he says that those who have never heard or seen the written law are still guilty for breaking it (Rom. 2:12).
Thus, if the moral law of God is implanted into man as Paul and evangelical Christianity claims, and if that moral law tells us that it is wrong to punish an innocent person, and God punishes an innocent person, then God has violated his own law.
One would have to conclude that either 1) the moral intuition that it is wrong to punish another person is mistaken or, 2) God's law does not apply to himself.
The problem with #1 is that it is virtually universally held that it is wrong to punish an innocent person for what someone else has done. While I have had some people dispute this in the comment section, I have never seen one example in which a judge or magistrate allowed a substitute to suffer the penalty owed by the guilty party. It just strikes us as wrong. The injustice of it is present even in the smallest child. Try punishing one of your children for what his or her sibling did (of which the former is completely innocent). I am sure you will get a cry of protest and rightly so. If the innocent child volunteered to be punished in the place of his or her sibling, that would be noble, but it would not serve the purpose of justice. The parent who punished the innocent child, even though he or she volunteered, would be committing an act of injustice.
The problem with #2 is that if the law does not apply to God, then it must be an amoral matter. In other words, if God is perfectly righteous, he could not commit an act that is immoral. If punishing an innocent is an amoral matter, then the entire law of God is amoral and thus useless as a standard of morality. The law would simply reflect what God orders man to do but would not reflect true or objective morality.
So, I conclude that the idea of the atonement (penal substitutionary theory), which is widely held in evangelical Christianity cannot be true.