You can safely uninstall or deactivate Real Time. Your saved games will not break. However, due to the changed citizens' behavior, the city might become unbalanced right after that.

Real Time settings for particular cities will remain in the city save files. If you reactivate or reinstall the mod later, the settings will be just reloaded.

The default settings are saved in an XML file located in the game's directory. It will not be deleted when you uninstall the mod. If you don't delete the file manually, the default settings will also be reused when you reinstall the mod again.