The pope did not make that comment outside the context of Gaudium et Specs or the Catechism. In all cases our consciences must be properly formed to be reliable.
CCC 1783 Conscience must be informed and moral judgment enlightened. A well-formed conscience is upright and truthful. It formulates its judgments according to reason, in conformity with the true good willed by the wisdom of the Creator. The education of conscience is indispensable for human beings who are subjected to negative influences and tempted by sin to prefer their own judgment and to reject authoritative teachings.
CCC 1784 The education of the conscience is a lifelong task. From the earliest years, it awakens the child to the knowledge and practice of the interior law recognized by conscience. Prudent education teaches virtue; it prevents or cures fear, selfishness and pride, resentment arising from guilt, and feelings of complacency, born of human weakness and faults. The education of the conscience guarantees freedom and engenders peace of heart.
CCC 1785 In the formation of conscience the Word of God is the light for our path, we must assimilate it in faith and prayer and put it into practice. We must also examine our conscience before the Lord's Cross. We are assisted by the gifts of the Holy Spirit, aided by the witness or advice of others and guided by the authoritative teaching of the Church.
CCC 1786 Faced with a moral choice, conscience can make either a right judgment in accordance with reason and the divine law or, on the contrary, an erroneous judgment that departs from them.
CCC 1787 Man is sometimes confronted by situations that make moral judgments less assured and decision difficult. But he must always seriously seek what is right and good and discern the will of God expressed in divine law.
CCC 1788 To this purpose, man strives to interpret the data of experience and the signs of the times assisted by the virtue of prudence, by the advice of competent people, and by the help of the Holy Spirit and his gifts.
Peace be with you
Indeed consciences must be properly formed to be reliable, and that should be a given, otherwise it would have even less weight, for rather than making conscience the supreme objective guide (as some contort Ratzinger as saying), i was careful to include that conscience "is not an autonomous and exclusive authority for deciding the truth of a doctrine," which is directly from DONUM VERITATIS.
Nonetheless, while following one's own conscience cannot legitimate dissent according to Rome (though the church began in dissent from authority), yet it allows dissent for even a theologian "who might have serious difficulties, for reasons which appear to him wellfounded, in accepting a non-irreformable magisterial teaching."
And thus while Ratzinger upholds the need for a correctly formed conscience, which V2 allows for even outside the church, his statement* does not seem to be restricting obeying conscience only when it conforms to Rome's teaching, but that basically for the individual conscience is a type of ultimate tribunal, not as the supreme objective authority, but because conscience is what man acts out of, and thus it is appealed to for obedience.
"But have renounced the hidden things of dishonesty, not walking in craftiness, nor handling the word of God deceitfully; but by manifestation of the truth commending ourselves to every man's conscience in the sight of God. " (2 Corinthians 4:2)
*Commenting on paragraph #16 of the above document, theologian Fr. Joseph Razinger (now Pope Benedict XVI) wrote in 1968:
Over the pope as the expression of the binding claim of ecclesiastical authority, there still stands one's own conscience, which must be obeyed above 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. (http://www.ascensioncatholic.net/TOPICS/morality/ConscienceAndMoralDecisions.html and see here )
cf. 16. In the depths of his conscience, man detects a law which he does not impose upon himself, but which holds him to obedience..(GAUDIUM ET SPES)