First, yes, there is a difference between CCD and CMOS produced images. Not only are there cosmetic differences, like the pattern the produce, but there are also operational differences. What is particularly critical is the signal to noise ratio of any given system, as cinematographers like to be able to shoot through as much latitude as they can. CCDs have very high uniformity, which is why they are very popular for HD units where a lack of uniformity can just look, well, awful.
Second, this is for motion, not still, and processing out raw files (even if you had that capability) would be so much data and time, it wouldn't be worth it. Thirty progressive scans per second, 3:1 shooting ratios? Besides, color isn't totally software dependent. The quality of the glass in FRONT of the chip makes a large difference in color as well.