[The United States] government has no business giving a whirl about "hurt[ing] the religious beliefs of others" (a standard both elastic and asymmetrical, virtually begging for a heckler's veto) and that there is no "universal right of free speech," at least in practice (as opposed to the philosophical principle, which I wholeheartedly endorse).
The fact is that the First Amendment, no matter how embattled, protects a range of expression unthinkable even in Western Europe. Because of that unique position, and because the U.S. seems doomed to play an outsized diplomatic and military role in the tumultuous Muslim world, it behooves the State Department to constantly explain the vast differences between state-sanctioned and legally protected speech in the so-called Land of the Free. If the U.S. government really was in the business of "firmly reject[ing]" private free-speech acts that "hurt the religious beliefs of others" there would be no time left over for doing anything else.
It's really not that hard. The values in that film (or "film") are not our values; our government respects religion, religious expression, and religious pluralism (including and especially that of Muslims, even in the wake of murderous Muslim-led attacks on American soil); and we are not in the business of approving or (for the most part) regulating the private speech of our citizens. To the extent that that message is not sufficient for rioters, the problem is theirs.
Some liberal Tweeters this morning are pointing out that, hey, the Bush administration condemned the Mohammed cartoons, too!, but this mostly goes to illustrate how bipartisan cravenness can be. We know that this issue will keep coming up; maybe it's about time the American government, and the rest of us, develop a more American response.