Frankly, it seems as if most people are missing the point. The guidelines from the American bishops regarding honoring pro-abortion politicians are (as has been pointed out to me by more than one legalistic authority, usually self-appointed), not binding in Canon Law. They are, however, morally binding. Further, "giving scandal" has always been and remains a serious sin. Actions that you personally might consider harmless or even praiseworthy need to be considered in light of their possible effect on others. As Jesus said, "It were better for him, that a millstone were hanged about his neck, and he cast into the sea, than that he should scandalize one of these little ones." (Lk. 17:2)
A school is presumed to act "in loco parentis" (in the place of the parents) to the students. As head of the university, Father John Jenkins is thus the head of "the Notre Dame family." It is his responsibility to see that students are trained scholastically and, more importantly, morally. He abrogates his responsibility and violates the trust placed in him by parents, alumni, faculty, supporters, and even the board of trustees (despite their approval) when by any word or act he suggests to those placed in his care and whose consciences may not have been properly formed that dissent from legitimate instructions from duly constituted authority is morally acceptable.
Ordinarily, whether one accepts the authority of one's religious superiors or even the doctrines of a particular religion is a private matter, or (as some seem to be saying), an "internal affair" of Notre Dame. Inviting the president of the United States to give a commencement address was and remains well within the right of any school, secular or religious, including Notre Dame. There is not only a place for free and open debate on controversial subjects, but a necessity for it if a school wishes to be worthy of the name "university."
Again, however, that is not the point. The guidelines established by the American bishops are clear: no Catholic university will for any reason bestow honors on pro-abortion politicians. Mr. Obama, for whatever reason, is pro-abortion. When this was first pointed out to Father Jenkins, he equivocated by claiming that he thought the instructions applied only to Catholic politicians, although that is not stated in the guidelines. When Father Jenkins' interpretation of the guidelines was corrected, he equivocated again, maintaining that he was proposing to honor Mr. Obama not as a pro-abortion politician, but as president of the United States, although it is difficult to understand how to separate the two. Further waffling and ambiguities followed.
The bottom line is that, although explicitly ordered not to do so, Father Jenkins gave an honor to a pro-abortion politician. This makes the whole issue one of simple honesty. If Father Jenkins does not believe what the Church teaches, or refuses to obey legitimate authority, he is free to leave. That is his choice. Father Jenkins may be absolutely sincere in believing that he did the right thing. He may be firmly convinced that the only way to advance the Pro Life cause is to dialog with pro-choice politicians, shower them with accolades, and insult anyone who disagrees with him or voices dissent from his opinion.
As an individual, Father Jenkins is free to do all this, and more. He is free to express any and all opinions, and believe anything he likes as long as he does not act on any belief that will harm other individuals, groups, or the common good — including giving scandal. The problem is that Father Jenkins was not acting in this instance as a private individual, but as an official representative of an institution that claims to be Catholic. He is therefore morally bound to act in a manner consistent with that position, or surrender it. It is a matter of complete indifference whether the trustees, the media, the student body, or anyone else approve his actions. As Edmund Burke pointed out in a different context in a speech to the Electors of Bristol in 1774,
Certainly, Gentlemen, it ought to be the happiness and glory of a Representative, to live in the strictest union, the closest correspondence, and the most unreserved communication with his constituents. Their wishes ought to have great weight with him; their opinion high respect; their business unremitted attention. It is his duty to sacrifice his repose, his pleasures, his satisfactions, to theirs; and, above all, ever, and in all cases, to prefer their interest to his own. But, his unbiassed opinion, his mature judgement, his enlightened conscience, he ought not to sacrifice to you; to any man, or to any sett of men living. These he does not derive from your pleasure; no, nor from the Law and the Constitution. They are a trust from Providence, for the abuse of which he is deeply answerable. Your Representative owes you, not his industry only, but his judgement; and he betrays, instead of serving you, if he sacrifices it to your opinion.By remaining as president after violating this sacred trust, Father Jenkins is being profoundly dishonest. He is using his position to undermine the Church's authority and teachings, especially with respect to those entrusted to his care. If Father Jenkins were employed in a business, he would justly be fired without notice for acting against the interests of his employer. In moral philosophy what Father Jenkins did is called "betrayal of a benefactor," a sin for which Dante, in his Infierno, reserves the lowest place in Hell.
Because Father Jenkins' dishonesty is open and public, and a cause of scandal, it is the duty of the American bishops who issued the guidelines that Father Jenkins openly flouted to engage in fraternal correction, and offer instruction to him to help reorient him in a more moral direction. To do anything less is to put any bishop who refuses to get involved in the same position as Father Jenkins himself. By his silence such a bishop consents to an act that he, as a member of the American Episcopate, had previously condemned, and concerning which a significant proportion of his brother bishops have already made clear is scandalous.
Nor can anyone, bishop, priest, or lay, use the presumed silence of the Vatican as an "out." Archbishop Burke, a high Vatican official, gave a speech on May 8, 2009 that I personally witnessed, and in which His Excellency declared in no uncertain terms that Father Jenkins' bestowal of an honor on President Obama was a serious error. By persisting in that error, Archbishop Burke stated, Father Jenkins and the Notre Dame board of trustees had placed the university in the position of no longer being worthy to be called Catholic. Even if Archbishop Burke had not spoken, however, the failure of others to act in what we believe to be a moral manner does not excuse us from doing what we believe to be right.
That being said, I also believe that the position taken by Mr. Obama at Notre Dame and the speech he gave opens up some potential avenues by means of which the Pro Life cause can make significant gains. This may even have been what Father Jenkins intended. Unfortunately, Father Jenkins failed to realize that he could have achieved the same end legitimately, without thumbing his nose at the Catholic Church and the Pro Life movement, simply by not bestowing an honorary degree on Mr. Obama. In any event, the end never justifies the means. Whatever Father Jenkins' good intentions, the fact remains that he gave grave scandal not just to Catholics, but to honest people everywhere, decreasing respect for all religion by his example, and undermining all moral authority.