I'd be concerned about the pellets making holes in the canopy.....maybe if you only give the rifle one pump??
Also do you intend to shoot each grain of sand off? sounds labourous.....

Seriousy though, let it dry and give it a shake whilst folding it up. Despite many commments about sand being abrasive etc etc, in reality, unless it is that NQ coral sand, your kite will be old and long since upgraded by the time sand wear becomes a factor.
I also suspect brushing (or blowing) sand out from behind the LE and other tight spots prone to wear - will cause as much wear as leaving it there to fall out next session. Just IMO though.
If you are set on using compressed air, I don't see any difference over brushing as long as you don't get the nozzle too close to the fabric.