I put a post on the CMUCam forum describing the problems I have with the CAM_RESET line on the CMUCam3 module. And one of the CMUCam developers kindly replied confirming my fears. That line is used to reset the OV6620 camera module, and needs to be pulled low and left along. So it can't be used as a GPIO line connected to the Pololu uDSMC reset pin :( I had thought about dropping in a transistor invertor circuit so that the CAM_RESET could be held low until a motor controller reset is required and a high pulse on that line could have reset the controller (with the appropriate HAL/OV6620 reinitialisation). But with that the mysterious half-voltage drop seen on the CAM_RESET line, it left me fearful of using that approach. Best to leave the camera alone to do it's magic.
The forum reply did make a great suggestion :) I'm only using two of the four servo outputs on the CMUCam3 (for the pan and tilt servos in the turret assembly), so have the spare two servo outputs for use as GPIO lines. I need to make some other cabling to hook it up, but great to have a proper solution for resetting the motor controller.
With that sorted I'm going to head back into the MMC code in the CMUCam3 HAL driver. Fingers crossed I can work out why the current code doesn't like the PQi MMC card I have, then onto fixing it..