First, let me say I don't attend church regularly, but always enjoy the experience when I do -- regardless of the type of service or religion.
I was raised Catholic, though definitely not strict, as my family did not attend church regularly. Our church had a crying room. Like LilJen's description, most parents/families knew when to take the child to the crying room. This church was NOT a mega-church, by any means.
Tolerance is a good lesson.
That means tolerance for children, special needs children and adults, the handicapped, and anyone and anything else, including so-called Mega-churches that choose to practice religion in a way that others may not agree with.
I hope this family finds a parish that accepts their child and where they feel welcome.