The Inconvenient Conscience - George Cardinal Pell

In the most recent First Things, there is an article by George Cardinal Pell called "The Inconvenient Conscience". After reading The Death of Character this article ratified from a Catholic perspective another problem with our understanding of morality, and that is, our understanding of our conscience.

He makes multiple statements about the subjection of the conscience to our feelings. E.g. The spirit must be moving if we feel good about the decisions. He might as well call this idolatry. He wonders why many people make decisions they feel good about, call it the Spirit's leading, but actually sin in acting out their decision. A good example would be the the girl in the movie "Saved" sleeping with her boyfriend because she thought Jesus was telling her to. This a completely irrational understanding of the conscience and the work of the Holy Spirit. Only when the feelings from the conscience line up with the Scripture, can we then think it is the Holy Spirit moving us. Pell adds that a persons conscience cannot go against the Catholic Church, or they must search themselves, the scripture, and be open to more conversations. The church has authority in his view (he is a good Catholic after all), and he is calling Catholics who hold divergent view on Abortion, the Death Penalty, and Contraception to a higher standard. This seemed to flow well from the thoughts of Hunter. Why do we do what we do?