I firmly believe that all authority should be questioned in the corporate environment. A good manager should have the wisdom to acknowledge that he can fail to see things that the developer did.
If you go by what Clubber proposed then:
* If the manager is right, the developer will notice the value of accepting the technical input of the manager and develop a keener sense of timing within the development process.
* If the manager is wrong, the developer will understand that he shouldn't just accept orders handed down to him and remain mindful of the impact of the changes he makes to the code because his opinion will be respected by the rest of the team.
Now the author mentioned that in his organization "There are processes in place to get things like this removed" so the issue might be more that the developer either doesn't know that the project exists or that it works. Only if it's the later and the manager is sure that refactoring is regularly performed the developer is wrong for his the insubordination.