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Look into Image Registration. --> http://en.wikipedia.org/wiki/Image_registration
The functionality is available under the opencv_contrib repo and works only with OpenCV 3.0.0. I think it will solve your problem. I know there is test code that aligns two images of the same spatial area and finds the difference between the two. It is similar to what you are looking for. The repo is here -> https://github.com/Itseez/opencv_contrib/tree/master/modules/reg
However this method does not employ the use of feature based (keypoint detection and descriptor matching) alignment and uses a more accurate pixel based alignment. It is up to you what method you want to use. You are on the right path with homography, alignment etc.
