Suppose a school had a rule that non-Christian children had to stay after school on Fridays to do the cleaning, and a Jewish child was punished because she needed to go home before sunset and therefore didn't stay. Would the fact that the other children were perfectly able to stay make the school's actions less unlawful?
If you remove your initial criteria of "non-Christian", and just said "children" it would be an almost textbook example of indirect discrimination.
Again, the real scandal is the Diocese being let off the hook. Because this will happen again.