I don't think there is enough information for me to answer your question completely; for example, I don't know what call you are making to perform the "image" "save", but I can guess:
FITS does not store RGB data like you wish it to. FITS can store multi-band data as individual monochromatic data layers in a multi-extension data "cube". Software, including ds9 and aplpy, can read that FITS data cube and author RGB images in RGB formats (png, jpg...). The error you see comes from PIL, which has no backend to author FITS files (I think, but the validity of that point doesn't matter).
So I think that you should use aplpy.make_rgb_cube to save a 3 HDU FITS cube based your 3 input FITS files, then import that FITS cube back into aplpy and use aplpy.make_rgb_image to output RGB compatible formats. This way you have the saved FITS cube in near native astronomy formats, and a means to create RGB formats from a variety of tools that can import that cube.