While this is not a GUI tool, my quick tests indicated that diffxml has some promise. The author appears to have thought about the complexities of representing diffs for nested elements in a standardized way (his DUL - Delta Update Language specification).
Installing and running his tools, I can say that the raw text output is quite clear and concise. It doesn't offer the same degree of immediate apprehension as a GUI tool, but given that the output is standardized as DUL, perhaps you would be able to take that and build a tool to generate a visual representation. I'd certainly love to see one.
The author's "links" section does reference a few other XML differencing tools, but as you mentioned in your post, they're all proprietary.
