Other thoughts.
I'm not sure why you're surprised the C->Python pickle/unpickle works. You've changed the type name from Element to _elementtree.Element, so I would guess Python always uses the C version to unpickle as well. Can you debug to verify what actually goes on under the hood? Why did you change the class name, by the way, I don't think it's a valid change at least for 3.3 in terms of backwards compatibility.
Regarding that compatibility, and even easier idea would be for the C pickle to return the same __dict__ implicitly gathered from the Python version, and then only one version of the unpickle is required.