Sadly there would be no way to do that on a device, if a device has root it will have sufficient privileges to read your Shared Preferences as well as your SQLite databases and even Account Manager if it wants to.
You can look into linux file permissions if you want to learn more but any device that has root will be able to access your shared preferences.
If there is sensitive data on in your Shared Preferences just warn the user that if there device is rooted they are at risk. Traditionally for example on Nexus devices if you want to root the device it will wipe the entire thing but on specific devices there are exploits that won't require a wipe so you might be at risk.
Hope that helps.