Hi Alex,
why do the tiny commander flashes bother you?
They would only be visible if the object is very close and shiny.
Let me try to illustrate...
The following picture was taken from a distance of about a meter away. If you look closely at the right eye, you will see a second much smaller light spot more to the center of his eye. That is from the commander-pre-flash.
The second sample is taken around 3 meters away from the main object, but even the grass right in front does NOT show any light from the commander-flash.
However, if you want to get sure then the only thing you need is a SG-3IR from NIKON. It is a piece of plastic that covers the pop-up flash and only lets the IR part through.There is no need for any expensive extra triggers etc.
I hope this info will help you with your decision.
Greets,
Matt