If in your shoes:
To my Daughter:
1. NEVER EVER leave school unless you are in physical danger and the school will not or can not protect you ("Columbine"). Anything less, you go and report to the Principles office. Once you leave the school grounds, you are open game to anybody that might want to hurt you.
2. CALL ME. No matter what I'm doing, I'll come (and you had better mean it and come immediately because that's VERY important.) Little girl's psyche is SOO fragile compared to a boy's, and their interacton with their Dad effect the rest of their life.
3. Some discussion about what the Pledge means to a lot of people, and that people that fought and died for this country might be inorder. But those same people fought and died for her right to leave out the "Under God" part, and if she wants to leave that out, still be respectful of others and at least have the decency to stand (as otherwise she's just looking for trouble) - there ARE consequences for the decisions she makes and she needs to learn that now - take drugs/get addicted; fool around/get pregnant, etc....
4. I'd take her back to the school right away and talk to the principal and the teacher. IF (and that remains a big IF until you've heard the other side) the teacher did this, then she was out of line, and it doesn't need to go any further than the teacher's apology (don't go sueing the school system over it).
This is the perfect opportunity to show your Daughter how a real man acts (the kind of real man you hope someday she falls in love with and marries).
Disclamer: Since my daughter is still only 9, I may not know what the heck I'm talking about.