Well, the court would not stop me from resigning from the school board in protest, but I hope the board appeals because this was not what the sep of church and state is about.
As far as J. Doe, the prayer at the start of a meeting is not likely to cause any religious indoctrination. I would guess she is far from any worry on this point. But the law of the land does not mean you can restrict others because what they do may offend you. I would have said, "Get Over It".
You'd think a group of ADULTS sitting down to a meeting wouldn't be in danger from one little prayer.