The contribution of the flash even in "controller" mode has been hashed to death and it most certainly is there. Whether it contributes enough to cause a problem for you is another matter, dependent on the relative power/position of your slave flash, and other things. Since I don't regularly take pictures of mirrors
, it doesn't bother me at all.
Perhaps the OP's question was more about eliminating any flash, including pre-flash, from the on-board flash. I can see this as being a more relevant issue, than arguing about how much contribution the controller makes, when taking pictures of people, who are sometimes bothered by the pre-flash and blink. Unfortunately, that is not possible, except by using an RF trigger. For all intents and purposes, this implies running the slave in full manual mode.
The new Cactus V6 RF trigger will allow some remote flashes to be remotely controlled with respect to power level, although strictly speaking, they are still running in a full manual mode, with no automation whatsoever. Some photographers prefer to shoot in full manual, but given the nature of the question, I am guessing this is not the solution the OP is looking for.