any chance you could to the same thing with texture replacement or render to texture? with scripting you take an existing ship texture, and then adds an alpha chanel (or modifies an existting alpha chanel). the script would slowly fade the alpha chanel to the desired opacity. with texture replacement you could have a series of textures, each with less opaque alpha chanels, and slowly go from one to another to another.
I think so. Just make a new texture, assign it to the ship's slot. Then every frame, clear the texture to black, and redraw the original texture on it with a decreasing opacity value. (gr.setOpacity()).
EDIT: Actually, that's incorrect. You'd need to completely clear the texture to...completely clear. Not sure how you'd go about doing that, though, hmm.