In order to forget private keys passphrase (id_rsa) i usually run:
ssh-add -D # to forget all loaded identities
ssh-add -d # to forget primary identity ($HOME/.ssh/id_rsa)
Now with macOS Sierra v10.12.1 i get this error:
$ ssh-add -D
All identities removed.
$ ssh-add -d
Could not remove identity "/Users/user/.ssh/id_rsa": agent refused operation
Could not remove identity "/Users/user/.ssh/id_dsa": agent refused operation
I searched google with no luck!