That would have been difficult given so many faiths and those not of a religious faith. People who could accept Scott's prayer, did. People who didn't, likely didn't bow their head and were respectful. This is a country with freedom of speech and freedom of religion. We can respect everyone especially during a time of mourning during which people tend to turn toward their God, or some type of hope.
And the song that followed his prayer was Imagine by John Lennon, including imagine there is no heaven, hell or religion. I didn't get upset about that. It represented the beliefs of some people and the show was designed to represent as many people as possible.
You can reply with your thoughts, with no debate from me.