GitHub recently has added support for images comparation (https://github.com/blog/817-behold-image-view-modes), althought is not possible to modify them. I think it would be interesting to have a somewhat similar functionality (at least "2-up" mode would be easy to do) and also it would be possible to add at a future version the posibility to modify them in images compressed with a non-lossy algorithm (png, bmp...) modifying the singular pixels, no advanced image processing.

I know it's not an easy feature and probably not useful for a lot of people, so i think it probably would be better to develop it as a plugin for Meld (althougth there's no plugin system at this moment, but i think with a try-import-except would work...)