Seems a little like saying, you burn some gas and your car goes, and if it goes 80mph, that's just physics. You can't make it illegal to obey the laws of physics? Plants are just biology and burning things is just chemistry. You can't make it illegal for a plant to grow and for a human burn it and inhale it, can you? Well...if you pass a law that pi=3 it doesn't change the nature of the universe, but it does regulate…
It's more like saying if you draw a picture of a car going 80mph, that's just a drawing. Doing physics or chemistry can directly harm people. Doing math or drawing pictures can't.
Like the article said analogies are no fun. I agree with your premise but not with your conclusion.
You will perhaps agree that encryption has the potential to directly harm people just as physics or chemistry?