Here is an excerpt from Cardinal Newman’s remarks “On Conscience” at
newmanreader.org/works/anglicans/volume2/gladstone/section5.html
QUOTE BEGINS:
I have already quoted the words which Cardinal Gousset has adduced from the Fourth Lateran; that “He who acts against his conscience loses his soul.” This dictum is brought out with singular fulness and force in the moral treatises of theologians. The celebrated school, known as the Salmanticenses, or Carmelites of Salamanca, lays down the broad proposition, that conscience is ever to be obeyed whether it tells truly or erroneously, and that, whether the error is the fault of the person thus erring or not [Note]. They say that this opinion is certain, and refer, as agreeing with them, to St. Thomas, St. Bonaventura, Caietan, Vasquez, Durandus, Navarrus, Corduba, Layman, Escobar, and fourteen others. Two of them even say this opinion is de fide. Of course, if a man is culpable in being in error, which he might have escaped, had he been more in earnest, for that error he is answerable to God, but still he must act according to that error, while he is in it, because he in full sincerity thinks the error to be truth. {260}
Thus, if the Pope told the English Bishops to order their priests to stir themselves energetically in favour of teetotalism, and a particular priest was fully persuaded that abstinence from wine, &c., was practically a Gnostic error, and therefore felt he could not so exert himself without sin; or suppose there was a Papal order to hold lotteries in each mission for some religious object, and a priest could say in God’s sight that he believed lotteries to be morally wrong, that priest in either of these cases would commit a sin hic et nunc if he obeyed the Pope, whether he was right or wrong in his opinion, and, if wrong, although he had not taken proper pains to get at the truth of the matter.
…
Antonio Corduba, a Spanish Franciscan, states the doctrine with still more point, because he makes mention of Superiors. “In no manner is it lawful to act against conscience, even though a Law, or a Superior commands it.”—De Conscient., p. 138.
And the French Dominican, Natalis Alexander:—“If, in the judgment of conscience, through a mistaken conscience, a man is persuaded that what his Superior {261} commands is displeasing to God, he is bound not to obey.”—Theol. t. 2, p. 32.
The word “Superior” certainly includes the Pope; Cardinal Jacobatius brings out this point clearly in his authoritative work on Councils, which is contained in Labbe’s Collection, introducing the Pope by name:—“If it were doubtful,” he says, “whether a precept [of the Pope] be a sin or not, we must determine thus:—that, if he to whom the precept is addressed has a conscientious sense that it is a sin and injustice, first it is duty to put off that sense; but, if he cannot, nor conform himself to the judgment of the Pope, in that case it is his duty to follow his own private conscience, and patiently to bear it, if the Pope punishes him.”—lib. iv. p. 241.
Would it not be well for Mr. Gladstone to bring passages from our recognized authors as confirmatory of his view of our teaching, as those which I have quoted are destructive of it? and they must be passages declaring, not only that the Pope is ever to be obeyed, but that there are no exceptions to the rule, for exceptions there must be in all concrete matters.
I add one remark. Certainly, if I am obliged to bring religion into after-dinner toasts, (which indeed does not seem quite the thing) I shall drink—to the Pope, if you please,—still, to Conscience first, and to the Pope afterwards.
QUOTE ENDS
As you can see, Newman allowed that under some circumstances it is imperative that people should obey their conscience before obeying the Pope. He believed that if the Pope ordered a priest to advocate in favor of teetotalism or the holding of lotteries, yet could not obey the papal instruction without doing what he regarded as morally wrong, then that priest should not so obey. Having said that, he respected the authority of the Pope as a “teacher of the moral law,” so much so that Newman could also say of the Pope, “The championship of the Moral Law and of conscience is his raison d’être.”
Newman’s argument is thus in favor of both the Pope and liberty of conscience.
In Catholic just war theory, the killing of noncombatants is prohibited, except when such occur as collateral damage to an otherwise just act of war. Could the use of condoms be allowed among married couples if their principle purpose were intended as an act of justice consistent with the sanctity of human life, with any interference with the unitive and procreative aspects of marriage not intended but regarded as collateral damage? That is, if collateral damage that involves the killing of lives is sometimes allowed, why not allow collateral damage involving the saving of lives (if indeed condoms could have this effect, which I doubt)? Would not some room for conscience in this regard be consistent with Newman’s argument?