I see the PoA story as the same kind of thing as a moment of silence, or a student-led prayer in a school. I used to think, "Well, as long as the school isn't enforcing any particular type of belief ... "
But then I read some stories from the bible belt. Jewish students; atheists; foreign students from eastern cultures who prcticed Taoism, Bhuddism, Hinduism; all receiving death threats because they chose not to stand and recite The Lord's Prayer in class, or before the football game.
While the constitution only specifies that they state may not support or establish a religion, when the state (or its agent, the school) sees that the majority is trying to impose its religious views on a minority while under state auspices, I think the state has an affirmative duty to protect the rights of the minority.
Does this mean I don't think City Hall can put out a manger scene near Christmas? No. No one will be singled out for not going to look at it. But at the same time, if there is a manger scene, then other faiths should be allowed to put up displays honoring their own sacred stories.
If I were in California, and my child didn't want to recite the PoA (or just the "under God" part), I would hope she could use it as a teaching point. When other students ask why she doesn't recite it, she can explain why. Maybe get them thinking about it. I have even read stories about teachers teaching this very lesson when students ask about it.
However, in the bible belt this could be dangerous. If I lived there I would hope someone in a more tolerant part of the country would do exactly what this father has done.