Do you intend to use the sonar unit to measure the distance between the object and the focal plane of the camera and set the focus based simply on distance or are you thinking of using image processing techniques to determine when the image is in focus? Both methods are possible, but the latter is practicably possible with the Arduino due to processing power, memory and bus, to name a few. Reading the sonar and adjusting the foucus using a simple look up table is within the capabilities of Arduino.
Using image processing techniques to perform the autofocus is possible with the processor on the Due, I am not certain that the Due hardware/software is stable enough to engage that large a project on.