I think the whole point of the .s command is so that it's a public acknowledgment.
If you were to make it so that .s were not public, you might as well just remove the .s command as a whole. You can just as easily .p a <S> to someone.
Seems odd to me that it bothers you enough to request a change, though. Out of curiosity, what does it matter? I find myself hardly ever paying attention to the chat buffer when I'm flying anyway.
But I guess if enough people think a fix is needed, the best fix in my mind would be to allow the user to either view all salutes, or just salutes directed to themselves. A check box in the options menu would suffice.
I personally think the public salute thing is neat.