What happens when a person becomes a believer is that conscience is purified by the Holy Spirit; and, as a Christian, I believe conscience is giving pure information. I believe that the Holy Spirit, in conjunction with your conscience, is going to send pure impulses. That's why a Christian who sins is going to suffer far more intense guilt than a non-believer who's got a seared conscience... The Holy Spirit will operate in and through your conscience and make moral judgments on your action.
John MacArthur