I enjoyed reading the article but I found the discussion somewhat confusing because the question drifted from the one above to one more like "Do I commit evil if I think I am doing good?" I believe that this is a distinct question. Genesis says that mankind obtained a sense of the difference of good and evil by disobeying God and eating of the fruit of the tree of the knowledge of goodness and evil. If there indeed is such a thing as a sociopath who can not process any concept of good and evil (either in his own thoughts or in reference to society's norms) then such a person has a remarkable cognitive mutation that sets him apart from the normal model of humanity described in Genesis. (I'm not an expert on the topic of whether such people do or don't exist). But, it's an entirely different matter to talk about doing evil because we convince ourselves that what we are doing is moral and right. Indeed, this self-rationalization is all too human.
When we ate of the fruit of the tree of the knowledge of good and evil, we disobeyed God and sin came into humanity. No part of our being is separated from that sinfulness, not even our post-Fall sense of goodness and evil. Thus while we all (perhaps except sociopaths) have a moral sensibility, that sensibility is not God's; it is our own and it is corrupted. Certainly people sometime make choices that they are aware (correctly) are or may be morally suspect. Dietrich Bonhoeffer wrestled with this very clearly when he decided to join the murder plot against Adolf Hitler. But, how many more times do we sin when (because?) we have convinced ourselves that we have the moral high ground? We see that Jesus knew that addressing this self-rationalization was part of his message of salvation: Yes, you believe that your brother has wronged you. Forgive him anyway. Or, as interpreted by Paul: Yes, this other person has wronged you not once but many times. Don't keep track of those wrongs. Sometimes it will the case that the other guy HAS wronged me; maybe in other cases it is self-deception. But it is all a warning that it is God, not we, who knows the true measure of good and evil.
The paradox of this is that our moral sense may be imperfect when compared to God, but it is not nothing. Most of us are not sociopaths, nor do we live in the amoral surroundings of the kill or be-killed struggle for survival in the animal kingdom. But I believe that among the actions of the Holy Spirit are: 1) Changing our utility function (what we want to do), and 2 ) refining our moral sense to give us a better idea of what God things is right and wrong. Maybe these are the same thing, but I think that they may be different.
In the year in which Inception became such a big hit, I realized in all the media discussions that I have a strong tendency to what is called lucid dreaming. I tend to remember many of my dreams, and when I wake up and I realize I've been dreaming I can sometimes decide whether to rejoin that dream as I go back to sleep. Last night, perhaps because I was thinking about writing this post, I had the strangest continuing dream in which I was an international forger of rare documents, on the run from INTERPOL. What the authorities didn't know was that I enjoyed the chase for for its own sake, and after I pulled off the forgery job, I always returned the originals, so I never profited directly and there would never be any evidence to stand up in court. In reality I don't even draw well, much less have any conscious desire to forge rare documents. I don't even know what documents would be rare, and I think I would enjoy being a fugitive from INETRPOL less than almost anyone I know. What this dream made me think about is this jumble of what we are capable of doing, what we may be inclined to do, and how this interacts with our imperfect sense of right and wrong. This is why the Bible tells us that we are different than other animals, and why the Bible is a story that tells us how God wants this strange interplay to turn out in the end.