Hi,
It is certainly possible to interface the camera and Arduino via USB host shield. Potentially your sketch could watch for the appearance of an Object Created event returned from a CanonEOS::EventCheck which would indicate a photo was taken since the last time that command was responded to, there's more info here.
I don't know this will give you tighter control than having the external intervalometer control the body and rig, but it sure does sound like an interesting angle to investigate.
Have you found another way since posting this question?
Geoff