Pretty straightforward suggestion, have an imput box in command blocks for a 'Password' that is set and then later changed by a command that you can only type if you have the highest permissions on a Server or the Owner of a Realm or LAN world. This way, repeating command blocks you want to be there will not log, but command blocks placed by anyone who types the password wrong or leaves the box empty will log, so you know when a nefarious command block has been placed. Hope everyone likes this idea and think it will be useful!
EDIT: Forgot to mention: Password can only be set/changed through chat commands, not blocks. And if you right click a command block with the proper password set, you cannot access it unless you type the password in. This way, they cannot just view the password and then change it, etc. Even highest perms have to do this, for extra security.