I think some of the confusion comes from the idea of "weilding" a weapon. I don't know what the official take on this is, but from my experience weilding for most characters has meant a weapon that either 1) you attack with, or 2) Kept ready to use for AOO.
In that fashion, if a character with a longsword and a light mace charged into a character, he could say "I'm not weildling the mace" in which case he doesn't assume two-weapon penalties. However, any AOO he got to make would have to be with his longsword.
If you applied this argument to the bow scenario, then while fireing your bow you could say that your weilding your fist. This would cause TWF penalties, but would allow you to have a threatened range. Or you could drop the bow, which automatically means your weilding your fists. However, on the next round, you could choose not to weild your bow. You could keep it in one hand, and suffer no TWF penalties with your fist, but then you could not fire the bow that round.
Just to note, if your using that system that are also other drawbacks to not weilding a weapon. I would also say that disarming that weapon would be automatic, or at least a big bonus, because your not activively working with it.
