Much as I enjoyed this article, the two different meanings of theory do not make it a homonym. I realize this is nitpicking, but if we're going to educate the public, we shouldn't give short shrift to exact meanings in other fields. An illuminating homonym is "left" as in "I left my keys in my left pocket" -- the same word, but completely different in meaning. Consider "law" -- a legal law and a scientific law are entirely different, but they spring from a common meaning historically, as theory does.
I could go off in a nerdathon about the innocent category of "figures of speech" -- metaphors, analogies, similes, even synedoches! If you study examples, you'll see they are all different enough that you might not want to misuse them :) even if in most situations you could probably get away with it. Although if you said "synedoche" people might look at you strange :)
Again, thanks for this piece!