A recent talk by Father Bob Pierson 1 quoted Joseph Ratzinger (as he then was, now Pope Benedict XVI) as saying that the individual conscience must overrule ecclesiastical authority. I was intrigued by Pierson's claim and looked up the original source, which is an early commentary2 on Gaudium et spes, specifically its Article 16. I've put the section quoted by Pierson in italics.
For Newman, conscience represents the inner complement and limit of the Church principle. Over the pope as the expression of the binding claim of ecclesiastical authority there still stands one's own conscience, which must be obeyed before all else, if necessary even against the requirement of ecclesiastical authority. This emphasis on the individual, whose conscience confronts him with a supreme and ultimate tribunal, and one which in the last resort is beyond the claim of external social groups, even of the official Church, also establishes a principle in opposition to increasing totalitarianism. Genuine ecclesiastical obedience is distinguished from any totalitarian claim which cannot accept any ultimate obligation of this kind beyond the reach of its dominating will.
I am finding the final sentence quite difficult to parse. It seems like he is saying that genuine ecclesiastical obedience does accept a controlling role for conscience. But then it sounds like one can simultaneously disobey and "genuinely obey", which is odd. Elsewhere in the text, Ratzinger speaks about natural law and the Golden Rule as standards to diagnose and reshape the "erroneous conscience", and it surprised me that he doesn't also mention the Church there. Overall, I think I am missing something basic which would help me to understand what he means in the passage above.
So: What relationship between conscience and Church authority does the Pope actually envisage?
I'm looking for answers that draw on his other writings, up to the present day - in particular, sources that illuminate what he personally thinks, as opposed to those which are primarily about what the Church as a whole accepts.
1. Video and transcript here; I'm linking to Daily Kos because they're the only site I can find which provides a text transcript, not because I endorse Pierson, Kos, etc. The original talk was on homosexual civil marriage, but this question is emphatically not; I'm not asking whether he's right or wrong, just using his quotation to ask a different question.
2. Monograph by Joseph Ratzinger collected in Commentary on the Documents of Vatican II, volume 5, ed. Herbert Vorgrimler (Herder and Herder, 1969). Translated by W. J. O'Hara from Das Zweite Vatikanische Konzil, Dokumente und Kommentare (1968). The quoted text starts on page 134.