How do I remove a preference (save password) set in the iCloud keychain?
The setting is in Safari, not Keychain.

Open Safari > Preferences... > Passwords. You will see a list of sites that is searchable. Under "Password" you will find some that say "never saved", select that item and click the Remove button. 

Basically Safari keeps track of the sites that will have remembered credentials, but they are securely stored in Keychain.