"This section is for shabiha, informants, collaborators, spies and homosexuals," said the warden, who asked to be named only Abu Abdo.
Abu Abdo, a former officer from Syria's foreign security service, insisted he was trying to reform rather than punish the prisoners by giving them regular lessons in Islam.
In fact, one of the judges explained that he and his colleagues are following a "Unified Arab Criminal Code" adopted by the Arab League, which is rooted in Islamic law.
"This basically follows sharia, while taking into consideration modern Muslim life," said Mohammed Najib Banna.
Banna, who had been a teacher in a religious school and a cleric reading sermons at a mosque, is now a judge in the council's Military Court.
"Our work now will prepare us for the day when the regime falls, because then there will be anarchy," Banna said.
While some of the detainees in the prison are accused of committing crimes on the battlefield, others are detained for charges ranging from adultery to prostitution and "disobeying parents."
This is especially true in the women's jail cell, where most of the inmates hid their faces under blankets during a visit by CNN.
Among the detainees was a teenage girl, the daughter of a couple who were both also incarcerated in the prison.
Some of the women were also accused of spying for the Syrian regime.
One woman stood and repeatedly performed a salute, accompanied by a martial stamp of her foot.
Asked who she was saluting, she listed the names of the father and son who have ruled Syria for 40 years: "President Hafez al Assad, President Bashar Hafez al-Assad."
"May God give victory to Bashar al-Assad," she said with a smile. "Because they're saying lies about him. He's likeable, excellent in every way."
Then she started saluting again.
Another 23-year-old woman who asked not to be named said she had been arrested 16 days previously for being a shabiha.
"I cooperated with the state while I was in university. I used to go and come back and communicate with them," she said. "And I would go to demonstrations supporting the president."
One might assume the United Courts Council had been formed to create a rival judicial structure to the Syrian government, which is believed to control a quarter to a third of Aleppo.
But a visit to the office of Gayed, the council's prosecutor, revealed political tension between rival rebel groups.
The suavely dressed former judge had a half dozen guests seated around his desk, most of whom were lawyers hoping to set up a similar court in the opposition-held northern town of Maraa.
There was also a stocky, bearded man dressed in a camouflage uniform who quickly excused himself after journalists entered the room.
"The man was here from Jabhat al-Nusra," Gayed explained after the man left. "He was asking me to hand over a prisoner to his court system. I said no."
Jabhat al-Nusra, or Nusra Front, is a well-organized Islamist fighting group. The U.S. government recently black-listed the group, accusing of it being a terrorist organization.
"We black-listed the Nusra Front because of its intimate links with al Qaeda in Iraq," said Robert Ford, the former U.S. ambassador to Syria, in an interview with CNN in Turkey.
"Nusra has a sectarian agenda ... (it) is anti-democratic and will seek to impose its very strict interpretation of Islam on Syria," Ford said.
But Gayed, asked about al-Nusra, called its members "our brothers in the revolution. They bleed for it. But we differ on how to build the state."