How many today have the needed skills to revert to such manual navigation?
“...the CSO could limit any possible damage by quickly shutting down the part of the system that looks like it might be under attack.”
That sounds ridiculous to this layman. You can’t shut down the Fire Control System or the Phalanx defensive system.
I think that is right. There are few backups. Shooting a .50cal machine gun at an incoming missile will not help.