I think too much fuss is being made about this movie by Christians and others who simply like to use the word contraversy in connection with it.
The movie itself has been watered down in its anti-religious tone, but that's not even the point. Is faith not to be tested? Do we think a mere movie with subtle anti-religion overtones will destroy our faith or our children? Are we so afraid of ideas that don't jive with our own that we have to shun or boycott presentations of those ideas?
And I think its the shrill denunciation of things that aren't explicitly pro-Christian that will create that backlash the author spokle about and rightly so. The exclusion of ideas that conflict our own is unhealthy and in the long run, counterproductive. Children who aren't exposed to both sides of the coin can develope an appetite for the forbidden fruit. The entire world is not an insular Christian community and that reality has to be faced, eventually. Better it not be a shock.