I don't think the command fall will accomplish what you want.
Webster's II New Riverside University Dicitonary (check other definitons to see how it could be interpreted)
"fall (v):
1) To come down without restraint, due to weight of gravity
2) to drop oneself to a lower or less erect position
3) to lose an upright or erect position
4) to descend from or as if from the sky 'The night falls quickly in the desert'
5) to come to rest, settle
etc"
Unless I am mistaken the affectted is free to follow the command as he sees fit.
So
1) is not an option since it outside his control and not a conscious action (he can't control gravity)
2) could be an option depending on the situation, basically if on say a flying carpet the affected would simply lie down.
3) Could also be an option by not being erect when flying the affected has already fallen
4) is likewise not an option since it is outside the affected's control
5) seems to be the option you want to get to
But like I said it depends - and unless I am mistaken the affected gets to choose which way to interpret the command and most often would choose the way most beneficial to himself.
Now going by what the PHB gives for choices and what happens the command fall seems to imply to fall to pron from the standing position. I agree qith the choice of Halt being the best choice to get the affected to stop flying.
While I think "Halt" might be the best option, the spell descriptor for "Fall" says that falls to the ground and remains prone and not just falls prone Also, the beginning of the spell reads that You give the subject a single command, which it obeys to the best of its ability at its earliest opportunity. If they are using a Fly spell, they have the ability to get to the ground and then fall prone.