The simmering tension came to a boil Friday when Williams, 44, and McGettigan, 62, argued on the 18th floor of the D.A.'s Center City headquarters, where the executive suites are, the sources said.
McGettigan, a respected former federal and state prosecutor whom Williams handpicked in January 2010, was expected to work his final day tomorrow, sources said, and was to be replaced by Ed McCann, the trial-division deputy district attorney.
"They fought, but they have fought before. It's like your parents fighting," said a second prosecutor. "He's [McGettigan] either out or he's on his way out."
"People are worried. It's a pretty big deal," said a third prosecutor.
"He's just not happy," a fourth prosecutor said of McGettigan.
"He's said that to me on several occasions. I don't think he likes the politics, people asking him for raises, the whole thing."
After failing to respond to repeated Daily News requests seeking confirmation of McGettigan's exit yesterday, D.A. spokeswoman Tasha Jamerson issued a media alert saying McGettigan was taking an extended medical leave starting June 6 to have hand and knee surgery and to rehab.
Jamerson did not respond to an email seeking clarity on whether McGettigan was expected to return to work.
Sources said McGettigan made it clear last night that he is not returning.
He will be leaving a lucrative job; his $166,400 salary tops Williams' $160,850 salary, according to city payroll records.
McGettigan was described by sources as a top-notch prosecutor who dislikes office politics.
"I've known Joe for more than 20 years," said defense attorney Fortunato N. Perri Jr., who learned only yesterday from a prosecutor that his friend was leaving.
"He's a lifelong prosecutor, a terrific trial attorney and a real hard charger."
Williams, reached by cellphone yesterday as he was returning home from Washington, referred questions to Jamerson. McGettigan did not return a phone message.
He and other city prosecutors have questioned several of Williams' hires, sources said.
Those included an assistant district attorney who was brought on despite having been arrested five times, four of which were for drugs; and an assistant district attorney who was hired in early May and fired two weeks later for failing to disclose that she was living with a criminal defendant.
Because the Daily News was unable to verify those allegations last night, the individuals' names are not being published.
"I was disturbed when I learned of these hires, like I was disturbed when I heard about the assistant D.A. who was sleeping with the drug dealer," said a prosecutor, referring to Assistant District Attorney Jennifer Mitrick.
The Daily News reported last month that Mitrick, 30, was pulled from prosecuting two men who had been accused of trying to murder an alleged drug dealer after it was learned that Mitrick dated the victim after the attack.
Mitrick is still employed with the D.A.'s office, Jamerson has said.
Defense attorney A. Charles Peruto Jr. said McGettigan, whom he has known for 25 years, became disgruntled when Williams' promise to let him have complete autonomy in running the office did not materialize.
"Joe is idealistic, completely honest, thinks every criminal charged with a crime should do life. But at the same time, he wouldn't do anything illegal," Peruto said.
"Seth is a politician. He's a well-meaning guy. But that is inconsistent with the idealist that Joe is."
Michael Hinkelman contributed to this story.