The other day he offered a reflection on the third of St. Francis's Admonitions, on obedience:
The Lord says in the Gospel: Whoever does not renounce all that he possesses cannot be my disciple; and: Whoever wishes to save his life must lose it.
That person who offers himself totally to obedience in the hands of his prelate leaves all that he possesses and loses his body. And whatever he does and says which he knows is not contrary to his will is true obedience, provided that what he does is good.
And should a subject see that some things might be better and more useful for his soul that what a prelate commands, let him willingly offer such things to God as a sacrifice; and instead, let him earnestly strive to fulfill the prelate's wishes. For this is loving obedience because it pleases God and neighbor.
If the prelate, however, commands something contrary to his conscience, even though he may not obey him, let him not, however, abandon him. And if he then suffers persecution from others, let him love them all the more for the sake of God. For whoever chooses to suffer persecution rather than wish to be separated from his brothers truly remains in perfect obedience because he lays down his life for his brothers. In fact, there are many religious who, under the pretext of seeing things better than those which the prelate commands, look back, and return to the vomit of their own will. These people are murderers and, because of their bad example, cause many to lose their souls. (FA:ED I, 130)
My brother analyzed the text by pointing out the three kinds of obedience: true, loving, and perfect. True obedience is abandoning oneself to the wishes of the superior, and doing any good thing which is not contrary to his will. Loving obedience is doing so when one doesn't agree that this is the best thing, offering the frustration and missed opportunities as a sacrifice to God.
But perfect obedience arises, paradoxically, when one--because of conscience--is not able to do the will of the superior but does not 'abandon him.' Perfect obedience is remaining with the brothers in the willing endurance of the awkwardness and difficulty of not being able to do the will of the superior. Such willingness to suffer rather than break relationship with the superior is laying down one's life for the brothers.
So it seems that obedience is located in the relationship with one's superior rather than in the particular will that is its expression. But how are these things separated? Certainly they are not distinguished in any clear way in practice. It's a mess, for sure, and accepting it willingly is perfect obedience.
Francis knows that freedom of conscience is a dangerous business for an institution, and so he concludes by saying that those who use it as a pretext are murderers who cause others to lose their souls.
Nevertheless, Francis, as always, presents a radical ideal. Our obedience is first of all to fraternity--making sense of what we say in our vows, I give myself to this fraternity with all my heart--even above the particular will of the fraternity expressed by the will of our superior.