To the atheist, the conscience is the end product of a long line of evolutionary and social conditioning, so when it bothers them, they are not really guilty of anything. As James Sire puts it, they are really only guilty of guilt. Feelings of guilt are the problem, not a violation of moral principles.
This is why we live in a culture of therapy. The goal is to rid ourselves of the feeling of guilt instead of the guilt itself. Unfortunately, we see this way of thinking finding its way into many churches as sin and the cross of Christ are ignored and replaced with a “Christian” self-help regimen. Our culture only wants good vibes and talk of sin makes us feel bad. All we really need to learn to do is to forgive ourselves. James sire goes on to explain the biggest problem with this approach.
“In a universe where God is dead, people are not guilty of violating a moral law, they are only guilty of guilt, and that is a very serious, for nothing can be done about it. If one had sinned, there might be atonement. If one had broken a law, the lawmaker might forgive the criminal. But if one is only guilty of guilt, there is no way to solve the very personal problem. And that states the case of the nihilist, for no one can avoid acting as if moral values exist and as if there is some bar of justice that measures guilt by objective standards. But there is no bar of justice and we are left not in sin but in guilt. Very serious indeed.”
-James Sire, The Universe Next Door
Churches and “Christian” materials, that neglect sin, guilt, and the atonement, and only focus on the therapeutic, not only fail to help those in need, they lock them into a worldview where forgiveness is unattainable. Even under the name “Christian,” empty deceit can hold sway.
See to it that no one takes you captive by philosophy and empty deceit, according to human tradition, according to the elemental spirits of the world, and not according to Christ. –Colossians 2:8
-D. Eaton
The Fight of Faith 