One of the much hated things that Lucas did to his own masterpiece series was to reduce the mystical Force to what seems to be nothing more than a simple case of biology through the introduction of the midi-chlorian. While it is true that it has long been established that at least some component of Force use has been related to biology, this concept was always left rather esoteric and undefined and expressed in things such as family blood lines, species abilities, etc.. While all of this would certainly fit with the concept of midi-chlorians it does a lot to dull the metaphysical claws of the Force. But does this have to be the way?
While it would certainly be easy enough to simply retcon the whole midi-chlorian thing in your own personal gaming, I believe there is a way to keep the concept but redefine it's nature. The vast amount of fiction written for Star Wars allows us many opening to do just that. There are several cases in the Expanded Universe where different life forms are given some sort of natural connection with the force. They sense it, feed off of it, even in some cases nullify its use. If you were to redefine the biological nature of the midi-chlorians they could still exist in the Star Wars universe, be used for most of the same purposes they have in the story but keep them from dealing such a brutal blow to the character the Force.
What if the midi-chlorians were not the source of the Force, but rather another Force-related life form that is present in the bodies of Force-using life forms. In this way it might be a measurable substance that would occur in differing levels dependent on how strong a being was with the Force. This is similar to how some forms of bacteria or algae are present in some plants and animals and can be used as a measure of the overall health of a life form. Now the Force is still a mystical energy that is not created by, but can be measured by the existence of midi-chlorians.
You could even take this further and say that the true nature of midi-chlorians is misunderstood in the Star Wars universe. Like many of our own biological secrets, it might only be partially understood to an extent where it seemed to be the source of the Force, and was officially accepted as such by the academic and scientific communities as a whole. Even the Jedi themselves might not be able to make the distinction because it was just too minute a difference. Alternately, the Jedi might perpetuate this misunderstanding as a way to further preserve their mystical appearances.
As I mentioned at the beginning, one could try to stuff the genie back in the bottle, but if you didn't want to do that, this would allow you to keep the concept and still allow the Force to be that magical thing that is was and rightfully should be.