Hmm ... I can see a clash between game-able abstraction and realism here. It's a difficult one.
I'd still be tempted to rule that only a close-combat weapon is lost. But that does open another can of worms in situations where the throwing weapons can also be used in close combat - as with your javelineer.
And there's another thing too. Say you've got a warrior armed with spear and shield who also has a sword at his side. Shouldn't he be able to sweep out the sword rather than have to run to where the spear fell? For that, I'd be tempted to rule that a model that is visibly armed with an additional weapon can draw it to lose the disarmed penalty at the cost of one action. That's not "fair" of course, but it'd be aesthetically satisfying.
Given that, I'd probably say that a warrior armed with several throwing axes or javelins can "rearm" at a cost of one action while still in close combat, just like the spear-armed warrior above. He doesn't need to spend the action when not in close combat, as he can revert to his smooth drawing/throwing action (which won't help him in melee). And the same goes for (say) a sword-armed man who also has some javelins.
It's a bit of a fudge, though!