Just weighing quickly, I'm afraid I haven't got time to read through the comments, just the OP and the link. So forgive me.
I see this as equivalent to flag desecration, which is protected by freedom of speech in the USA. If the chruch wants to burn a copy of the Quran in protest then let them do so. But I fully expect retaliation, as the OP said people are already protesting in Indonesia. Pretty much all religious people see their religion as above any significant form of criticism. It's kind of sad, we don't really get this to such an extent with other things such as politics.
Anyway, I think the church has the right to do this and in some ways I can respect them for it, but I do kind of think it is an antagonising douchbag thing to do at the same time.
