I've had almost exactly the same idea about image compression, but I didn't even try because of what Blizz said.
About your idea of separating the graphics into 'packs': RGSSAD is already protecting the files. If updating small portions is really the concern, we could just script something that would read the RGSSAD archive AND some other source (the "Graphics\" folder structure, or a ZIP file containing the folder structure). That way, you release the game with the RGSSAD file. If you want to upgrade or add graphics, you simply release a ZIP file containing the pics in proper hierarchy as in the Graphics folder. The script would give preference to this additional source, so any new files are used instead of using the ones from the RGSSAD archive. Of course, if you want to encrypt the updates, simply use an encryption module like DREAM.