Daily I create a clone of my system disk using Carbon Copy Cloner and this is working nicely. However, having a clone connected to your Mac may present a problem in starting apps automatically, for instance at startup. In some cases OSX will start the app from the clone rather than from the system disk. One of the examples is 1Password, which has a little component, called 1Password Mini, which is starting automatically for each user. The app is not listed in the login items. 1Password Mini is often (or always ?) started from the clone and other components of 1Password, interacting with 1Password Mini (such as the update process) will notice this and issue a message. I wonder if there is a way to force apps to be launched from the Applications folder on the System Disk and ignore the one on the clone. Taking the clone offline is not an option for me.
The cleanest (and safest; see below) solution would be to set up Carbon Copy Cloner to automatically mount the clone disk/partition before the backup starts and unmount it once the backup is finished. See: https://bombich.com/kb/ccc4/performing-actions-before-and-after-backup-task
Not only would this prevent the problems you have described, it would also protect you a bit better against ransomware, which unfortunately made its appearance for the first time on OS X a week ago, because your backup would only be vulnerable during the daily cloning window and not all the time.
Short of doing something radical such as stripping the executable rights from all your files on the backup disk (which would also break the backup), I don't see how you could prevent applications to be launched from it, and even that might not prevent helper code to be executed by a main application.
What you could do is add the backup disk to System Preferences->Spotlight->Privacy. That would at least prevent you from accidentally launching apps from the wrong disk yourself using Spotlight (or launchers that rely on Spotlight such as Alfred).