There is nothing particularly difficuly about reading CCDs. Yes you get an analogue output, but then you just stick it into an ADC and work with it. You do need to generate a multiphase clock, usually three phases, all square waves clocked 120 degrees out of phase, and you need to keep careful track of which clock you have reached.

I play with large area CCDs for astronomical imaging and I am working with that new EZ-USB processor family to build a new camera for my telescope. Area CCDs are even more fun !

Steve