Is it all that important to return the instance in the DifferentialGeometry? It seems more straightforward to just apply the appropriate inverse transform on hit point and normal vector on the way back out.
In my ray-tracer (Glome), I treat instances as just a container for some other object along with a transformation matrix, that itself behaves like a regular object. Every kind of object has a method to construct a bounding box, so that when building an acceleration structure that contains instances, if I remember correctly, I take the 8 corners of the bounding box of the contained object, transform them, and constructs a new bounding box around the transformed points. It's not optimal, but it works okay.
Another way of working around your problem is to just pass the current instance (or a list of instances) as an argument to your ray intersection function. (I use a similar trick for textures, and also for a tagging scheme where I can apply arbitrary tags to objects and then pass back a list of all the tags of objects that the ray hit when I return a ray intersection.)
https://github.com/jimsnow/glome