Hm, I'm wrong. You can't do that with referenced objects.
One possible way is to unload existing reference but keep anim curves. Then load it again under different namespace and assign curves. It shouldn't be to hard to write this.
Btw, why do you need to rename objects? If you have name clashes you can group all objects from each referenced file together. That will virtually create a kind of a namespace.
When grouping referenced object just take care to select only nodes that are on top of the hierarchy.