I don't know... I'm completely with you on the sadly common misunderstanding of the word "theory" in scientific contexts, and there's really no defending the Season 8 clusterfuck, but using the word "theory" to mean "slightly qualified guess" in regular conversation is pretty widely accepted and has been for a long time. The word has two different meanings depending on the context. That's exactly why creationists et al can get away with the "It's just a theory" nonsense.

That said, it would be fun to do a Serious Scientific AU of that scene. Let's see, Giles as Newton, Buffy as Einstein, Willow as Feynman, Tara as Hawking, Xander as Bill Bryson, and Anya as an Intelligent Design supporter... :)

JESUS! JESUS, IT MUST BE JESUUUUUUS! ...Or maybe aliens.