They have had the policy in place for some time and they do apply it consistently. The Church is employing a very clever advertising campaign which has resulted in them being plastered across the world. They literally could not have paid for better advertising than they've received off the back of this very clever campaign.
In a TV story on this they said that the church had discussed the campaign with the advertising agents in the middle of the year and the agents had no problem with it then, so just when was this policy introduced?
If the policy was in place when the church first approached the theaters and the church wasn't warned, then I think they have a right to ask for their production costs back