In almost 29 years of practice in Florida, this is a situation I have never come across before now.
Disestablishment of paternity in Florida is covered by Florida Statute 742.18. Unfortunately, the provisions of the statute do not cover the situation that your nephew faces. I do not have access at the moment to case law to see if the issue has come before the Florida courts.
You may have to create your own Motion to Disestablish Paternity, which would state the facts as you have alleged them above, attaching the paperwork from the criminal matter. I suspect that CSE may still pursue the matter, arguing that the child has needs regardless of the circumstances of its conception. If CSE does continue to push the matter, contact the local TV stations and newspapers and feed the story to them. If they hit the angle of the state trying to punish the victim of a crime hard, it may cause CSE to back off.
I suggest that if at all possible you obtain an attorney to assist with this. If you cannot retain and attorney, I would think that the ACLU or Legal Aid would be interested in helping, but if not, and you live in a city with a law school, the school may have a free clinic that can give you assistance. If you even live near a city with a law school, contact the school and speak to someone about the case, as this is the type situation that should greatly interest them because of its technical legal mature and the greater issue of "punishing" a victim..
I hope this helps and answers your questions. Please click Accept so that I may be credited for my assistance. Thank you and good luck to you and your nephew.