Freedom of Conscience
(III) The Fallible Conscience

Freedom of conscience in the political sense is the right to act according to one's conscience free of governmental prevention, interference, or subsequent sanction. Conscience itself can be defined as the act, or acts, by which we judge, approvingly or disapprovingly, our conduct in the light of our rational moral knowledge. Conscience in this sense is not infallible. It can err either because the facts of the case requiring our action or inaction are insufficiently known, or because an intricate conflict of obligations resists a correct solution within the time at our disposal, or because our general state of ignorance, our lack of intellectual training and imagination, our moral obtuseness and spiritual perversion, will produce false judgments. . . .

We never know our objective duty because we are not omniscient with regard to the actual situation; we sometimes know a subjective obligation because one or more of the obligations from which we have to select our duty may be simple enough for us to know with certainty the action morally required by what we believe to be the facts of the situation;  and we always know our putative duty because we always can form a moral estimate (although exposed to moral error) of what is demanded by what we believe to be the actual situation. The fulfillment of putative duty is conscientious action.

At this point the difficulties begin. In order to be moral, action must be conscientious;   a will that deviates from conscience is immoral. Even if his conscience is badly in error, a man must follow it. Does liberty of conscience in the political sense mean that every man must be left free to follow it, even if it advises him to organize a revolution of Fifth Monarchy men or of the proletariat? If we say No, we are back to persecution for the sake of conscience. And since the practice of Western statecraft in fact has said No, the so-called freedom of religion and conscience has never been opposed as a "principle" to medieval persecution. The difference between "persecution" and "freedom" is one of degree;   some consciences that would have been persecuted in the Middle Ages are left free in the modern national state —but not all of them by far.

CW VOL 11,
The Oxford Political Philosophers, pp 33-34.