I think it went like this:
1. The case falls in Nifong lap as he is about to be defeated. He see an instant political leg up in the primary. He also believe the case because he has Mangum claiming she was raped, DNA, and might well expect to be able to get a defendant to deal. [He might at this point figure Mangum was raped, but knows she can not ID anyone. He feels he is safe as he has that DNA.]
2. Then the DNA comes back not matching any of the lacrosse players. [It is at this point I believe Nifong became a criminal.] He knows Mangum has lied to him about recent sex and unless he is just clueless, he finds out about what she does for a living. His case has fallen apart yet he will lose the primary IF he does not come up with indictments in it. So he forces a false ID. He goes to the grand jury and gets his indictments because he is already building a defense against the coming legal actions against him.
3. He wins the primary just bare with just enough votes to win a not have a run off.
4. He has hung himself out to dry. He has a great opportunity to drop the charges before the Cheek or any other petition drive gets any momentum. But he knows he is a criminal. He is afraid of these powerful families and thus does not dare drop the charges. This was really Nifong's missed opportunity. Had he taken it he would have avoid 60 Minutes and lots of other bad publicity coming his way.
5. Once Cheek got on the ballot, Nifong was locked in until at least election day. No way he drops these charges until after election day.
That leave the great imponderable in the mess. Why did Nifong except the designation of the case as exceptional and allow it to go to a judge who he has less influence on? What did Nifong get or what was he afraid of that made him accept this change?
Perhaps he sees a greater likelihood of a judicial dismissal with this judge, which lets him off the hook to some extent, coupled with the fact that he did get the indictments, especially if Mangum recants at an opportune time or announces through counsel that she will not testify due to emotional distress or mental illness.
But most likely there is something going on behind the scenes relating to your question that we are simply unaware of right now.
Great analysis!