If KNOX is running and says the device is secure, then it's actually secure. The KNOX make sure there is no application installed that tampered the system storage. These so-called spy applications have to be installed on the system partition to gain access to various functions of the phone. KNOX also allows you to scan your device for intrusions.
Additionally, save the data from phone and then perform a factory reset using Settings > Backup and Restore > Factory Reset.
