Conversely how do you interpret "let us pray" into you have to pray?
In addition, I have heard, Please remove your hats for the national anthem but never have heard "bow your head".
When I was in High School, when someone died or such as that we had a moment of silence during an assembly. Some people prayed silently while others just remained quiet out of respect for the dead or used the time to reflect.
Rick, I'm pretty sure you know that there are people who have left their family's religion but keep that a secret to avoid potential (and sometimes very likely) negative consequences. In an ideal environment, everyone would be able to act according to what their conscience dictated without worrying about getting chastised for it, but realistically, such an environment is all too rare.
When a school, a public institution (as I take it that we're talking about public schools and not private ones), considers it acceptable for some students to pray while others wait until the ritual has been completed, what kind of situation do you think that puts a student who has left his or her religion in? It is inevitable that, at one point or another, such prayers will happen to be those prescribed by a religion that someone in the classroom has left, especially if it's the majority religion in a given area. So if a student or students sat down and didn't partake in said prayers, it would put them in a situation where they either had to divulge their leaving the religion or make an excuse not to pray if someone asked them why they didn't participate in the ritual.
Do you think that's the sort of thing schools should allow or encourage? I keep seeing arguments against that kind of thing get framed as "atheist preaching," but the actual issue is a far cry from that when you consider certain scenarios that are both very real and very critical for some people.
Perhaps a good way to see the issue from another angle is to imagine yourself in the situation I explained above and think about what that would be like, placing aside your current stance temporarily.