I officiate flag football, which means I'll often do 7-8 games in a row in one day. Often times I'll have a splitting headache at the end of the day due to all the whistles, whether I use a Fox 40 or an Acme. Short of earplugs or not blowing the whistle (not an option, since I usually work R - what I wouldn't give to be at the U position!), is there anything to alleviate these symptoms?

Whistle only if you have to.
 

I'm assuming you will have at least 4 officials.

Only the covering official should whistle the play dead.

The other officials don't have to whistle unless you are the referee and you have to blow the ball ready for play or the players call a timeout.

Hold the whistle in your hand. This will force you to think before you put it in your mouth.

One other thing that may help, is when you are blowing the whistle and do not have to use your hands to signal simultaneously, cup your hands around your mouth and whistle, creating a megaphone effect. This does a great deal to preserve your hearing when you are able to do so. Obviously you will need your hands most of the time, and will not be able to use this, but every little bit helps.

Try using a lower tone whistle