I always thought he actually swallowed the bug and just kept going... until I read this thread today. That's funny, I've shown it to friends and they were impressed. "Damn! Freeman can stay in character all right!"
I thought that maybe being the film buff Spielberg is, he was inspired by this scene from Leone's Once Upon a Time in the West
<iframe width="560" height="315" src="http://www.youtube.com/embed/RupWSnWKD4s" frameborder="0" allowfullscreen></iframe>
They put honey on Elam's lips to attract the fly. Thought they did the same in Raiders.
Now I find out it was just coincidence and editing fun.
Learn something new everyday. True.