Visitors to SNUG's new headquarters on Lenox Avenue wrote messages of support. View Full Caption DNAinfo/Jeff Mays

HARLEM — The head of one of the city's anti-violence programs — staffed by ex-gang members who act as mediators — was arrested last week for beating a former employee and threatening to kill her, officials said.

Harlem SNUG, one of 14 sites that Mayor Bill de Blasio and the City Council are spending $13 million on to help reduce gun violence in New York's toughest neighborhoods, is also under a probe by the Manhattan District Attorney's office for threats and alleged drug dealing.

DNAinfo New York is withholding the names of the defendant in the domestic violence case to protect the identity of the victim, his ex-girlfriend. Both were employees at Harlem SNUG.

The supervisor is facing charges of assault and harassment in Bronx Criminal Court.

In an interview, the victim says that Mission Society, which manages SNUG, was aware of her claims of abuse and did nothing.

"They knew what I was going through," the woman said.

The alleged victim also claims she was forced to work in the same building as the defendant where it was impossible for them to avoid running into one another even after she showed Mission Society the restraining order she had obtained against him.

The arrest is the latest issue facing the Mission Society of New York City, which runs 20 percent of the 14 sites that are part of the Gun Violence Crisis Management System that de Blasio launched in August 2014.

The troubles come as the city is experiencing an uptick in shootings. NYPD statistics through April 5, the most current available, show a 7 percent increase in shooting incidents from this time last year and a 4 percent increase in shooting victims.

DNAinfo New York reported last week that the Manhattan District Attorney's office is investigating the shooting of a former employee at Harlem SNUG (which is guns spelled backwards) as well as allegations that the program still had active gang members, some of whom may have been engaging in illegal activities such as drug sales.

Sarah Solon, a spokeswoman for the Mayor’s Office of Criminal Justice, said Mission Society is doing a "deeper investigation" into the domestic abuse allegations.

The results of the investigation "could lead to termination" of the employee in question, Solon said. The individual is still employed pending the findings of the investigation.

Mission Society receives $1.4 million in funding from the Mayor's Fund for New York City, the Department of Health, the Health and Hospitals Corporation and the City Council to run three SNUG sites in Central Harlem, East Harlem and The Bronx.

Modeled after Ceasefire Chicago, the program uses former gang members to stop violence by hosting mediations and working to convince gang members to abandon the thuggish lifestyle.

The former SNUG employee who made the domestic violence complaint claims she was brutally beaten by the suspect, described by those who knew him as an influential former gang member who was passionate about his work.

According to the criminal complaint, on Sept. 4, 2014, the suspect punched the victim in the face and body. He then tossed the victim to the ground and dragged her by her hair through her apartment, telling her "I will kill you," court documents said.

Pictures the woman says she took after the alleged beating incident show bruises on her legs and arms. Court documents say she suffered lacerations to her lip, hands and face along with swelling and bruises to all those areas.

The victim says the defendant's promotion to supervisor of the city-funded expansion site in The Bronx occurred after the alleged beating.

"It's like no one wanted to do anything about what was happening to me," said the victim who, like several longtime Harlem SNUG employees, was recently fired. The Mission Society would not comment on personnel decisions.

Scott Simpson, the suspect's lawyer, did not respond to a request for comment. The defendant also could not be reached for comment.

Charlie King, a spokesman for the Mission Society, said the agency was aware of the supervisor's arrest.

"My understanding is that he was arrested and was released. It's the policy of the Mission Society not to comment on any personnel matter," King said.

The defendant was arraigned in Bronx Criminal Court on April 14 and released without bail. An order of protection was issued.

The victim said she was forced to work in the same building with her alleged abuser until he was moved to a new site after being promoted. King refuted charges that the Mission Society ignored the alleged domestic abuse and the victim's restraining order.

"The Mission Society does comply with any and all court orders and directives on any matter," King said.

The Mayor's Office of Criminal Justice has met with Mission Society leadership on multiple occasions over the last month to help them implement protocols around hiring and personnel management, city officials said.

Elsie McCabe Thompson, former head of the Museum for African Art and wife of former comptroller and mayoral candidate Bill Thompson, was named head of the Mission Society in April 2014.

She has declined repeated interview requests.

The city has also been meeting with DOH officials to ensure they are providing proper "monitoring and enforcement" of those protocols. The DOH and other community members sit on a panel that interviews the ex-gang members before they are hired to ensure they are no longer involved in the gang lifestyle.

The Rev. Vernon Williams, a well known anti-violence activist in Harlem and gang expert, said it does not appear that protocols were being followed.

Mission Society, a 200-year-old anti-poverty and social services agency does not seem equipped to run a program of this nature, he added.

"When you put administrators in place who don't know how to supervise employees who are just themselves coming out of the gang lifestyle, it's no surprise that there will be havoc," Williams said.

Brooklyn Councilman Jumaane Williams, chairman of the council's Task Force to Combat Gun Violence, believes the model being used by the city works.

The 14 groups around the city are already meeting to discuss the issues at Harlem SNUG and how to avoid them, he said.

"We have to make sure hiccups don't mean failure," said Williams. "That means we need to make sure the protocols are in place and are being followed."