Not sure I've understood your problem correclty - will try anyway
I guess your currently working with images from middlebury or something similar. If you want to use similar algorithms you have to rectify your images because they are based on the assumption that corresponding pixels are on the same line in all images. If you actually want depth images (!= disparity images) you also need to get the camera extrinsics.
Your setup should have two cameras and you have to make sure that they don't change there relative position/orientation - otherwise your rectification will break apart. In the first step you have to calibrate your system to get intrinsic and extrinsic camera parameters. For that you can either use some tool or roll your own with (for example) OpenCV (calib-module). Print out a calibration board to calibrate your system. Afterwards you can take images and use the calibration to rectify the images.
Regarding color-noise:
You could make your aperture very small and use high exposure times. In my own opinion this is useless because real world situations have to deal with such things anyway.