I saw that scene in the movie, but I believe it wasn't accurate. A seemingly definitive account of the murder of John Favara is given on ganglandnews.com. He was apparently slugged upon leaving a diner, stuffed into a van, and made to disappear. The movie shows Da Bull whacking him under an overpass, but in ganglandnews' version, Da Bull had nothing to do with it. (Of course, it's possible that Da Bull was involved, and that federal prosecutors simply gave him a pass on that murder because all the other murders that he admitted to involved mob figures, not civilians. If he admitted to being involved in Favara's murder, the jury in the Gotti case in which he was the key witness might have turned against Da Bull.)
Gotti and his family were in Florida, establishing alibis. It is inconceivable that Favara's murder could have happened without Gotti's order, or approval.
Another inaccuracy: in the film, Gotti orders the murder of the cokehead who was with him and Angelo (Quack-Quack) Ruggiero in the assassination of James McBratney, who kidnapped and whacked Carlo Gambino's nephew. In real life, the cokehead was killed by a Westie in revenge for McBratney's murder.