The conscience and the Holy Spirit are not the same. A defiled conscience finds fault where there is none. It operates in a negative prejudice projecting one's own lack of faith in God's Spirit onto others. It is said that to the pure of heart all things are pure but to the defiled and unbelieving, nothing is pure. Indeed their minds and their consciences are defiled.
It reminds me of a story I once heard about Richard Nixon's Father. Richard Nixon said that when he was a boy, there was to be a family gathering at their house, complete with many Aunts, Uncles, and cousins of all ages. He then went on to say that in anticipation, his Father went about the house leaving coins of differing value laying about, that could be found by the children. At this point in the story, I pictured what a nice man Richard Nixon's Father was in seeking to bring joy to some little kid who would find a coin. But then Richard Nixon continued by saying that when he asked his Father why he was leaving coins laying about, the Father replied, "I want to see whose children are thieves".