Personally, I would have complained about a monthly "Bible Man" assembly at a public school. "Christians" forget that not everyone interprets the Bible the same way. Bible Man represents one way of doing that, but that does not mean it is my way. Nor do I believe that anyone should be forced to attend a particular interpretation of faith. I cannot believe that any school administrator would even think that it was a good idea.
The atheist parent is well within her rights to complain. She is 100% correct that even if children can opt out that they may be ostracized for that. No child should have to explain complex religious matters to say why he wont sit next to his friends in assembly.
I have a professional acquaintance, an atheist, who is constantly posting stories of horrible things people of faith have done with the line "Religion does no harm, right?"
He is right. People do horrible horrible things in the name of faith.
Oh, and if you happen to live in Altamont, TN in the Coalmont Elementary School area: you know who the atheist parent is; invite her to dinner and apologize for all the people who wear crosses and do not know what they mean. No proselytizing! And you can even skip the blessing, God understands.