Isn't what you're proposing exactly what led to this being a major problem? The automated systems disabled themselves, so people had to use the manual way, which was much less efficient, and 1,500 flights had to be cancelled.
They are referring to air crew procedures, not ATC. WHen the crew of an aircraft encounter a failure that doesn't have a common simple response, they consult a procedure book. This is something professional crews are well acquainted with and used to. The problem in the article was with the air traffic control system. They did not have a proper failback procedure and it caused major disruptions.
Their fallback procedure was "do it the manual way". Just like for the pilots. They thought it was a proper one...
This entire subthread is more a response to the suggestion that "The" solution is fuzzing your entire stack to death.