Archbishop Blase Cupich has gone on record at a Synod press conference, saying that "Conscience is inviolable", and that “If people come to a decision in good conscience then our job is to help them move forward and to respect that." Apparently this also applies to people who are living in adultery or who are committed to an immoral lifestyle, because "I think that we have to make sure that we don’t pigeonhole one group as though they are not part of the human family, as though there’s a different set of rules for them. That would be a big mistake." (Audio below.)
The Most Reverend Archbishop seems to be suffering from a serious lapse of moral judgment—all the more serious, because his error is so basic. Conscience is an individual's ability to judge what is right according to the moral law. As with any human ability, it can be strengthened or weakened. We can see clearly, or fail to see at all.
One of the effects of sin is the darkening of the intellect. You can read about this in St. Thomas, and (interestingly) in St. Paul's Letter to the Romans: "Just as they did not think it worthwhile to retain the knowledge of God, so God gave them over to a depraved mind, so that they do what ought not to be done."
Furthermore, the theory proposed by the Most Reverend Archbishop is condemned explicitly by St. John Paul II in his encyclical Veritatis Splendor. I am not one to quote John Paul II, but let me say, this passage hits the nail on the head.
Certain currents of modern thought have gone so far as to exalt freedom to such an extent that it becomes an absolute, which would then be the source of values. This is the direction taken by doctrines which have lost the sense of the transcendent or which are explicitly atheist. The individual conscience is accorded the status of a supreme tribunal of moral judgment which hands down categorical and infallible decisions about good and evil. To the affirmation that one has a duty to follow one's conscience is unduly added the affirmation that one's moral judgment is true merely by the fact that it has its origin in the conscience. But in this way the inescapable claims of truth disappear, yielding their place to a criterion of sincerity, authenticity and "being at peace with oneself", so much so that some have come to adopt a radically subjectivistic conception of moral judgment.
As is immediately evident, the crisis of truth is not unconnected with this development. Once the idea of a universal truth about the good, knowable by human reason, is lost, inevitably the notion of conscience also changes. Conscience is no longer considered in its primordial reality as an act of a person's intelligence, the function of which is to apply the universal knowledge of the good in a specific situation and thus to express a judgment about the right conduct to be chosen here and now. Instead, there is a tendency to grant to the individual conscience the prerogative of independently determining the criteria of good and evil and then acting accordingly. Such an outlook is quite congenial to an individualist ethic, wherein each individual is faced with his own truth, different from the truth of others. Taken to its extreme consequences, this individualism leads to a denial of the very idea of human nature.
John Paul continues later on with the following:
It is always from the truth that the dignity of conscience derives. [...] It is possible that the evil done as the result of invincible ignorance or a non-culpable error of judgment may not be imputable to the agent; but even in this case it does not cease to be an evil, a disorder in relation to the truth about the good. Furthermore, a good act which is not recognized as such does not contribute to the moral growth of the person who performs it; it does not perfect him and it does not help to dispose him for the supreme good. Thus, before feeling easily justified in the name of our conscience, we should reflect on the words of the Psalm: "Who can discern his errors? Clear me from hidden faults" (Ps 19:12). There are faults which we fail to see but which nevertheless remain faults, because we have refused to walk towards the light (cf. Jn 9:39-41).Then he says this about the role of the Magisterium with respect to conscience formation:
The authority of the Church, when she pronounces on moral questions, in no way undermines the freedom of conscience of Christians. This is so not only because freedom of conscience is never freedom "from" the truth but always and only freedom "in" the truth, but also because the Magisterium does not bring to the Christian conscience truths which are extraneous to it; rather it brings to light the truths which it ought already to possess, developing them from the starting point of the primordial act of faith. The Church puts herself always and only at the service of conscience, helping it to avoid being tossed to and fro by every wind of doctrine proposed by human deceit (cf. Eph 4:14), and helping it not to swerve from the truth about the good of man, but rather, especially in more difficult questions, to attain the truth with certainty and to abide in it.Now go listen to the Most Reverent Archbishop again.
[The transcript and context for Cupich's remarks are presented at LifeSite News.]