This seems to be a spicy issue in the Catholic blogosphere (e.g. this one from Vox-Nova and this one from Pro-Ecclesia) so, I'll take the bait.
Here is the main problem, as I see it: Commencement addresses in the U.S. have become mired in the politics of the modern academy and the propagandist relations of academia to the bought-and-paid-for dynamics of Washington.
If this were simply a public lecture, then, there would be little room for outrage. After all, dissenting views and rigorous debate ought to be a hallmark of any healthy university. However, this in one of "those" lectures, or should I say, after-the-fact stump speeches.
I feel that commencement addresses by presidents and other politicians, CEOs and other executives, and TV personalities, ought to removed altogether. But, certain politicians, execs, and TV personas may also have a contribution to offers to the academy. And, this may (and I give a very shaky 'may') be the case with this president.
One of the oddest things to me about Obama's campaign was the omission of his decorated academic career. If his speech were limited to an academic discussion of whatever subject is his expertise, then, that would be wonderful. But, sadly, I highly doubt that. He will be there as "Mr. President."
In that case, I think it is the wrong choice to make. I know for a fact that inviting G.W. to say anything at a University is an academic abomination. This is a different case, but, still, nonetheless, it seems like a bad idea to me. Notice, that the brand of ideas the person brings has very little to do with my evaluation of what is appropriate at a university. Much less a catholic university. As far as I'm concerned, any university that is not catholic, isn't really a university to begin with.
One major factor I chose to leave out of this discussion is the implication of giving someone an honorary degree. I still cannot get the bad taste out of my mouth from puking after witnessing Raymond Arroyo get an honorary degree while selling his book on Mother Angelica in his speech at my undergraduate commencement ceremony. Yuk.