It's really hard to replace *all* occurrences of a particular swatch with another, what with the one-hundred-and-ten ways of using one. (I made that number up, but go ahead and count'em. Don't forget to include the gap color of a Continued Footnote rule.)
Deleting a swatch and replacing it with the new one *is* recommended, and your way of first duplicating the original is actually quite smart.
I guess I could write a script to provide an interface to this, but it would essentially do the same.