When using the popup flash in commander mode, the popup flash contributes a little bit to the exposure even when disabled ("--"). It is possible to block the popup flash completely by using an SG-3IR infrared panel or infrared filter. Even if you don't have an infrared filter, however, you can make the popup flash invisible by using a shutter speed that is higher than sync speed. That's because the popup flash cannot do high speed sync therefore the popup flash will be blocked by the rear curtain. The popup will still be able to control the CLS slave.
Note: there are third-party flashes such as the Nissin Di866 that can be controlled by CLS but cannot do remote high speed sync. This trick won't work with such units.