Would it be so hard to come up with a retcon that says "The midi-chlorians are microscopic parasites that infest multicellular carbon-based life to feed off of their Force energy. Midi-chlorians cannot be removed from their hosts, as midi-chlorians alter the DNA of their vessels, making them dependant on the microbes for their continued survival. Midi-chlorians do not create or channel the Force, though they do have the potential to wield it; experienced Force users can harness that potential and put it to whatever work they desire through manipulation of the midi-chlorians"?

Hell, unlike most retcons, this wouldn't be like cutting a square peg to fit a round hole; it pretty much can work with what's already been established rather easily.