Hi, kind of late with this response, but I'd like to add some info. In my situation, using an Ikelite housing, a 6" dome port and a 17-40mm Canon lens, there is no option for manual focus. There is one gear ring, for the zoom only. I set the camera up for only one focus point and use auto focus. Once in a while without thinking, I might focus on the background, snap the photo and without noticing until it's too late that the main subject was slightly out of focus.
I just posted that while shooting u/w video with the MkII, I'm getting strange noises, I suspect the focus motor. Since my 7D, previous to the MkII would not auto focus while shooting video didn't make this noise. Right now I'm editing the noise out in post, but it would be nice if it was never there. I'm not sure what other options there are, to turn auto focus off, but that was a feature that I wanted when I moved to the MkII.