Complete authenticity is not required, of course, but gratuitious anti-Church comments that don't advance the plot are simply silly.
Two possible explanations come to mind - 1) the makers of the film are anti-Christian and so naturally think this way; adding such comments helps them express themselves or 2) the makers of the film think the comments will make the film more popular. Both might be true, or perhaps just one. Or maybe there is another explanation.
But it seems to me that no one would get away with gratuitious slaps at Islam, Buddhism, Judaism, etc. in a movie today without a ruckus being raised.