They should sing it. I see no reason not to. If buses arrive during it have the students stand where they are (or if necessary exit the bus and stand there). I do not believe in God, and have no problem singing "God save the Queen", it is just one word, and think what you will of it. And most non-Christians still have a God, it doesn't say Jesus or anything.
That is wasn't our national anthem until 1980:
Nothing was, not even God Save the Queen. It was used as such well before 1980 though. I don't know when it started being widely used, but it was well before then.
In elementary school we sang it every morning and the start of any afternoon assembly. I think every Canadian should, sure it might just gloss over most of them, but some take it to heart, then or in the future. It is our national anthem, just showing a small piece of pride in our country. Overt pride in our country is rather uncommon and I think we should do more to promote it, not to the scale of the US, but more than it is. I find that most people don't know the words to O Canada.
At my school also sang God Save the Queen after our weekly assembly, and when I went to high school, nobody from any other school even knew the tune. That is despicable. It would be even worse if our national anthem goes the same way.