A former student of mine wrote to me with a query on about how institutional Church authority could co-exist with the authority of individual conscience. She argued that ultimately my conscience will decide whether the authority is to be trusted, and quoted Anscombe as saying that one cannot help but be one's own pilot.
This made me think a bit more about conscience and authority. I had recently been reading about the Charles Bonnet and Musical Ear syndromes. In these, visual or hearing loss, respectively, apparently causes the brain to confabulate visual or auditory data, respectively, to fill in the sensorily deprived blanks. In Charles Bonnet Syndrome, the sufferers see things like colored patterns, faces, cartoons, etc. In Musical Ear Syndrome, they are apt to hear music. The significant thing about both syndromes is that the sufferers are quite sane and fully realize that the incorrect sensory data they are receiving is mere hallucination (that the hallucinations are limited to a single faculty must help there). They may, however, be distressed due to worries that they are insane, particularly if they are misdiagnosed by a psychiatrist, as in a case I recall hearing of.
A reasonable sufferer from one of these two syndromes will accept the testimony of reliable others that what she visually or auditorily perceives isn't there. In so doing, she is genuinely being her own pilot. Indeed, if she were to uncritically accept the visual or auditory data, she wouldn't be being her own responsible pilot: she would be replacing considered judgment with the flow of experience. Likewise, my colorblind son defers to the color judgments of others; an object may look light green to him, but when others testify that it is light pink, he accepts their judgment, and in so doing exercises his epistemic autonomy.
I think something similar can and does happen in moral matters. We have moral intuitions. These moral intuitions can be more or less reliable. But of course raw moral intuitions do not have a final say. Even apart from authority, moral intuitions need to be harmonized. And it may turn out that the best moral theory fitting the bulk of one's moral intuitions can go against some of one's moral intuitions, and then a judgment must be made.
Moreover, there is nothing contrary to being one's own pilot in making a reasonable judgment that a family of one's moral intuitions, or even all of one's moral intuitions, are less reliable than the testimony of an individual or institution one has reason to trust. That is just much an exercise of one's epistemic autonomy as it would be to accept the moral intuitions over that testimony.
I think that sometimes we confuse conscience with moral intuitions. The deliverance of conscience is an all-things-considered judgment of what is morally to be done. It may take moral intuitions into account, but it may also take other relevant data into account as well. The deliverance of moral intuition is not, as such, the deliverance of conscience, though of course in the absence of evidence against the moral intuition, conscience is apt to reasonably accept the content of the moral intuition as true.
It is quite possible for one to reasonably come to the conclusion that one's moral intuitions are less reliable than the teaching of an authority. In such a case, when there is a conflict between one's moral intuition and a teaching of the authority, one's considered moral judgment will at least typically go with the teaching. (I say "at least typically" to leave open the possibility that, say, a particularly strong moral intuition might be judged more likely to be accurate than a teaching that the authority gives quite low weight to.) In so doing, one may very well be a responsible pilot of one's self, if the reasons for accepting the authority as reliable were very good ones.
And one is not going against conscience then. On the contrary, in such a case, it would go against conscience to follow the moral intuitions, because one's considered judgment is that the authority is more reliable than the intuitions.
Our moral intuitions while being a genuine source of moral knowledge are often distorted by the desire to find excuses for our own faults or, more excusably, those of friends. Moral intuitions should not be glorified with the name "conscience". Like a Charles Bonnet Syndrome patient, one can be reasonable in judging that one ought to submit to the judgment of another, and then the other's judgment is the deliverance of one's conscience.
At the same time, I should note that normally our moral intuitions will play a significant role in figuring out that a putative authority should be listened to. When the putative authority's teachings harmonize particularly with those moral intuitions that we take to be more reliable, that will count in favor of the claim to authority, and when they disagree, that will count against the claim to authority. Here I think there is a useful rule of thumb: moral intuitions that something is permissible are less to be trusted than moral intuitions that something is impermissible. An action is impermissible provided there is a conclusive moral reason not to do it. An action is permissible provided that there is no conclusive moral reason not to do it. Generally, perceptions of absence are less to be trusted than perceptions of presence. Moreover, the space of reasons is large, and to judge that none of the infinitely many considerations in that space gives conclusive reason not to do A is fraught witih difficulty. (Of course, judgments about permissibility are very often right, but perhaps only because of the base rate: most actions people perform are right.)