There is no "free speech" issue here. Unless you want to argue that the regulation requiring a performance permit is, but then it ain't their job to enforce selectively depending on whether you or they agree with what the performance is. It's their job to enforce, period.
Alright. I agree it's not a free speech issue. The selection of song and the constitution of the choir make it easy to make this an 'emotional' argument. You are right that regulations are regulations and it is security's job to enforce the regulations, else mayhem and chaos could ultimately reign. BUT
I, alas, would be the security guard who said "Sure, go ahead" and would no doubt be out of job this morning, because there is nothing this chorus wanted to do that seems inherently harmful or an invitation to others to do anything harmful or disturbing. The kids probably thought of it on the spur of the moment, maybe on the bus on the way there or maybe once they had begun touring the memorial. It was their gift, their offering, to the victims and the country. It was one song, not an advertised 'performance' and took no skin off anyone's nose. That's what I hate about bureaucratic rules sometimes. They hire people who can think and use good judgment in a pinch, but then they aren't allowed to use it.