I looked at the Wire library and the only function missing is the empty constructor. I downloaded the source files Wire.h, and Wire.cpp from Github and added an empty constructor. It is a brain-dead attempt to see if the problem can be easily fixed. It looks like someone is trying to add a feature so there may be other parts of the library that are still broken.
I would have tried to compile it myself but when I went to download 1.5.6-r2 the server 503'd me. Anyway, I've attached the modified source files here if you want to try them out. Just put them in the Wire library folder under the SAM folder.
As another option you might be able to copy the entire Wire library from the AVR library subfolder and paste it over the one in the SAM folder. Unless the Due has some unique hardware for doing I2C it might just work.
Wire.cpp (10 KB)
Wire.h (2.92 KB)