Unless we want to eliminate the right of gov't employees to freely express their religion (and Graham is not an employee, just an invited guest) and/or put restrictions on what they can say on their own time regarding religion, or outlaw religious criticism altogether, I don't see how it is fair to single out Graham for his beliefs and expressions by deeming him "unqualified" to lead a service for a Christian holiday just because he thinks Islam is wrong and Muslims are mad about it.
Religion, by its very nature, is not an "all of the above" practice (nor is any deeply held conviction on any issue). You can't claim freedom of religion exists while not allowing people to disbelieve other religions (and freely say so).
Let me point out that Bush also held a Ramadan service (I think it was) and Christians didn't get to pick the attendees.