There's a problem with your argument (replacing 'copyright' for 'trademark' as others have pointed out).
What level of name protection applies to command-line tools? For example, can the GNU project replace existing Unix tools with their own implementations which have the same executable name?
yes, absolutely they can. In fact, they almost certainly DID! GNU's legacy was in creating tools that were compatible reaplcements for Solaris/Unix/etc ones.
What level of name protection applies to command-line tools? For example, can the GNU project replace existing Unix tools with their own implementations which have the same executable name?