Kelly is accused of using his fame to recruit young women and girls into having illegal sexual activity.
The network also announced a documentary on accused sexual abuser Jeffrey Epstein and a follow-up special to "Surviving R. Kelly."
Darrell Johnson's departure came after he said in a CBS News interview that he would "absolutely not" want his daughter alone with the accused sex abuser.
Darrell Johnson insisted it wasn't "a contradiction" to defend the disgraced R&B singer and accused serial sexual abuser, who faces new federal charges.
The disgraced R&B singer and accused serial sexual abuser was indicted Friday on 18 federal charges, after also facing numerous state charges.
The new charges address longstanding rumors that the disgraced R&B singer paid off the family of the girl in his infamous child sex tape.
Asante McGee, Lisa Van Allen and Lizette Martinez helped Lifetime's Brie Miranda Bryant accept the award for Best Documentary.
The R&B singer faces decades in prison if convicted.
Cook County officials have already filed 10 counts of criminal sexual abuse against the singer.
The new documentary program will be hosted by award-winning journalist Soledad O'Brien.
The R&B singer, who's been charged with criminal sexual assault, performed early Sunday at a club in Springfield, Illinois.
Kitti Jones, Asante McGee and Lisa Van Allen, three of the women featured in "Surviving R. Kelly," expressed gratitude that they have been "heard and believed."
Cook County Associate Judge Lawrence Edward Flood allowed cameras going forward in Kelly's trial and pretrial hearings, including the next hearing on March 22.
Gardner, who was rescued by her mother in a gripping scene in the docuseries "Surviving R. Kelly," said she doesn't think he should go to prison.
“I thought it was a real moment," Darrell Johnson said.
The "Saturday Night Live" comedian equated the church's sex abuse scandal with the singer's in a "Weekend Update" bit.
Gary Dennis, a nursing home worker from Pennsylvania, said he discovered the video while cleaning out an old box at his home.