I know everyone is eager to discuss midichlorians some more, so I was trying to tie it into Episode 3. Based on the canon material from TPM, we know that these jedichlorians allow the people to hear the will of the force -- obviously the good side. Jedi have higher concentrations of them, so they hear it better and can tap into it better than average joes. We also are led to believe the jedichlorians fathered Anakin (We've already shown how ridiculous this idea was, but it is canon, so I'll go with it for this thread).
It is a logical conclusion, thus, that the midichlorians are good. They work for the good side, they filter the force, maybe so jedi only hear the good side broadcast. They knocked up shmear so she could give birth to the chosen one (true, nobody knows what "chosen one" or "bring balance to the force" mean and probably never will).
So if the midichlorians are good, then how does a jedi turn to the dark side? Even someone with an evil will could only hear the good side broadcast to them, so they could never tap in to the dark side. In Anakin's case, he is crazy and in need of psychiatric help. The jedi should have seen this and had him committed, but even though they were too arrogant, Ani still shouldn't have turned with all those midis in him.
Did the midis just get lazy? Was it simply a case of parent neglect? They were too busy to spend time making sure he only heard the will of the good side? In the new ROTJ the dramatic scene could have dialogue between Anakin and Luke such as: "I'm sorry I wasn't a better father, Luke. Your grandfather, my father, the midichlorians weren't always there for me when I needed them. I must have picked up some of his. . . er. . . their bad habits." Geez, I guess just realizing your dad was a bunch of microscopic parasites would be enough to drive most folks crazy.
The only other thing I could think of is maybe there is a separate intracellular particle that allows people to hear the will of the dark side. Someone once jokingly coined the term "sithosome", so I will use that. Since all people have jedichlorians, maybe they all have varying quantities of sithosomes, too. Maybe Anakin had an unusually large concentration that eventually conquered his jedichlorians and took over his will. Since everyone has some concentration of each of these, then free will really wouldn't matter much. Every evil thought or action could simply be the result of sithosomes acting like that devil on your shoulder, and vise versa for the jedichlorians. What an interesting concept!
Oh well. If anyone has ever read RLS's Jekyll and Hyde -- or just the last chapter, then that is how I think GL should have handled the situation of Anakin's turn to evil. I suppose that is against GL's nature, though to use superior writers for his stories.