Following that reasoning, so long as one person complains about any prayers in the board meeting, that practice should be discontinued.
Absolutely.
How about majority rules? If the vast majority of Board members want to hear prayers, why shouldn't they? If one person doesn't, and everyone else wants to, why should the one rule the many? One person can (a) leave, (b) come late, (c) not pay attention, etc. If I were attending a religious gathering which preaches some things I do not follow or agree with, I am polite enough to just sit through it, as I sometimes did with my elderly mother. If I were attending a function and a prayer was offered by a religious representative of a religion I do not follow, I would politely sit there. Most well brought up adults would do the same.
People don't know how to be respectful and polite, and respect the religions of others? What's with this hair trigger intolerance?
Since the vast majority of people in the US believe in God in one way or another, why should the tiny minority of atheists rule who gets to say what and when? I don't think so.
And as for witches, when a large percentage of US citizens follow Wicca, get back to me at that point.