I think in choosing to create a public discourse about the state of Islam, the director is presenting more of a threat to the religion than if he indiscriminately destroyed a monument in a superficial action movie. This whole thing is actually a pretty smart political choice on his part, because in refusing to include the scene and then talking about it, he is able to single out the religion as corrupt without the fear of being personally accountable.
Technically, he hasn't committed any great injustice towards the Islamic faith - In fact, he's gone out of his way not to. Instead he's letting everybody else do the talking without putting himself on the line.
I gotta say, though, honestly I'm not entirely sure even Islamic extremists would ever target a useless Hollywood film director for showing the destruction of multiple competing religious symbols. There is no overt anti-Islamic sentiment, and that is what scares these people. People like Theo Van Gogh and Ayaan Hirsi Ali - who is still alive, by the way - directly condemn the ideology and that is why they are individual enemies of the faith. Emmerich just made a mindless disaster movie.
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