Exploited children
When small innocent children -- who are too young to have any say or to have developed a point of view -- are used in a film to carry out a theme of bastardizing a religion, in this case Catholicism, it is wrong. These same children may grow up one day to become Catholic, learn that they helped a false film narrative debasing their faith, and had no one to protect them from doing so.
The director had a narrative to tell, and to heck with the legacy -- perhaps of shame and regret, certainly of religious bigotry -- she would hang on the future of these children.
Even if you agree with the anti-Catholicism of the film, is it really fair to hang it on the children acting in it when you know they may grow up resenting it?