The weight will only come into play if its exceeds or encumbers the Air Elemental's weight capacity, otherwise the player can theoretically fly high up and then eject the creatures for fall damage, but keep in mind that.
a) The whirlwind lasts for 1 round for every 2hd air elemental has, so the player may be unable to effectively get to a height to kill the creatures.
b) All creatures get to make a save throw to avoid taking the damage of the whirlwind and a save to prevent being picked up by the whirlwind.
c) Only creatures one size category smaller can be picked up by the Whirlwind and the whirlwind created is the same size category as the elemental making it regardless of actually whirlwind size.
d) Flying creatures make a save to leave the whirlwind every round they are stuck in it.