Hi Bobby,
Yes, I think it should work. I've attached an image using an image map shader and a water shader (for the "glass", obviously). The image map shader uses the same image in the docs, where the red areas are transparent in the alpha channel and the green are opaque. So this might work for you if you have a stained glass image with an alpha channel for transparency. I would have thought you could achieve the same thing using an image without an alpha channel masked with a greyscale image for transparency though.
Regards,
Jo