When I was working on the S5IS port it took me a while to find the proper variables for the focussing system, so I 'disabled' it for a while. When zooming, focus did nothing. I can turn off autofocus partially, it'll still focus when I half-press the shutter-button but it will NOT do that when the camera is set to manual focus (button). It's still on my todo list but it should be possible to enable MF, as the firmware can also do that. It's even possible to let CHDK 'press' the MF button for about a second when starting the camera, so it'll be in MF mode all the time. Other systems can be bypassed similarly. We have the firmware, the firmware controls the entire camera so we can control the entire camera as well. It just takes some time to figure out everything.
I don't really know how you're planning on focussing by the way, it's quite tedious to do it with the buttons IMO. I guess you have a focus ring + additional lens on the body you're planning on putting the camera in?