I'd like to provide a well reasoned argument against the coordinated waving hands during free throws, since most people here who ***** about CA can't seem to think of one.
Having people concentrate on watching a sign and trying to time their arms to the movement takes away their focus on making noise. I think that any sort of coordinated effort in that regard is going to take away from the noise factor. If that's okay, then by all means stick with the waving. Just understand that it will most likely be quieter than otherwise.
I think it might work as well to hand out something to the students to have them wave on their own, and simply give the direction to be loud. Perhaps that isn't an option, though.
I also think the contrast that someone drew to the student section at football games is an interesting comparison. The culture of the student section is different in some way, where football games you're meant to go crazy, but basketball requires some higher level of civility. I'm not sure what you do about that, and honestly whether or not those at the top of the athletic department want it.