I have a similar problem... I have an OV5648 MIPI CSI camera. I've read on some other forums that no one has gotten the 10 bit bayer to work properly.
How is your image quality? All I can seem to get out of mine is something like this. I'm outputting data from the cam at 1280x720 and this frame is 1280x720 but you can obviously see I have some issues.

What sort of kernel modifications have you made?
I suspect, but cannot confirm that you need to make some changes to how the IPU sets up the channel buffer in the CPMEM (the offset and width parameters, specifically) See chapter 38.4.2.3 and 38.4.2.10 in the RM. I would definitely appreciate any input you have to solve my camera issue.
Another note: Depending on your camera, the extra 2 bits of those 10 bits might just be noise, and won't offer you a better image.