Convicted murderer John Connolly’s prayers to the newly sainted John Paul II were apparently answered yesterday when two Florida judges ruled the disgraced FBI agent’s second-degree murder rap should be tossed. 
 
 The lawyer for the former handler of notorious Southie mobster James “Whitey” Bulger told the Herald his client has been waiting for such a day. ||||| A Florida state appeals court overturned the murder conviction of corrupt FBI agent John J. Connolly Jr. on Wednesday, ruling that jurors relied on a flawed charge against him in the 1982 killing of a Boston businessman. 
 
 The decision raises the possibility that the 73-year-old Connolly, James “Whitey” Bulger’s longtime handler and a central figure in one of the most notorious chapters in Boston’s criminal history, could be freed. 
 
 By a 2-to-1 decision, the Miami appeals court ruled that Connolly’s conviction of second-degree murder with a firearm in 2008 should be overturned because, among other reasons, he did not carry or discharge the gun that was used to kill John Callahan in South Florida. 
 
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 The court appeared to fault prosecutors for overreaching. In their effort to win a conviction against Connolly, who had been 1,500 miles away in Boston when hit man John Martorano killed Callahan, prosecutors used a firearms charge that skirted the state’s statute of limitations. 
 
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 “It was undisputed that Martorano used his own gun to shoot Callahan and that Connolly never carried, displayed, used, or threatened to use the murder weapon,” Judge Richard J. Suarez wrote for the majority. 
 
 In 2009, Connolly was sentenced to 40 years in prison after jurors heard he had tipped off Bulger and Stephen “The Rifleman” Flemmi that Callahan would probably tell the FBI that the Boston mobsters were involved in the 1981 murder of World Jai Alai executive Roger Wheeler in Oklahoma. 
 
 Mary Callahan, the Florida victim’s widow, reacted sarcastically to the ruling. 
 
 “It’s a good thing that somebody gets something good out of this, because we sure didn’t,” Callahan said. 
 
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 “It’s interesting that he has a chance to be free and to be back with his family. Unfortunately, my husband doesn’t have that chance, and, as his family, we don’t have that chance.” 
 
 Callahan’s bullet-riddled body was discovered in the trunk of a parked car at Miami International Airport. 
 
 Callahan had persuaded Bulger to have Wheeler killed because Callahan was skimming some of the World Jai Alai profits and wanted to keep the thefts secret and possibly take over the business, Martorano testified during Bulger’s federal trial in 2013. 
 
 In Wednesday’s ruling, the appeals court judges sent Connolly’s conviction to a lower court, where it will stay “until any and all post-appeal motions are final,” according to the decision. 
 
 Florida Attorney General Pam Bondi is considering an appeal to the state Supreme Court, her spokeswoman said. 
 
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 Public defender Manuel Alvarez, who is representing Connolly, said he filed an emergency request to release his client immediately, but the court denied the motion later Wednesday. 
 
 “This conviction is a nullity,” Alvarez said. “He is now 73, and we are trying get him out.’’ 
 
 A spokesman for the FBI field office in Boston declined to comment on the ruling, since the case is still pending in state court in Florida. 
 
 Manuel Casabielle, Connolly’s original defense lawyer in Florida, said he was always confident that the former agent would prevail on appeal. 
 
 “In fact, I told John right after he was sentenced not to worry because we had already won the case,” Casabielle said. “I believe he was a scapegoat for the government’s use of the top-echelon informant program that was in place for the FBI back in the ’70s and early ’80s, when John was running Bulger and Flemmi. When the negatives of that program came to light, I believe John was hung out to dry.” 
 
 That murder conviction was the second time Connolly had been found guilty of charges linked to the Bulger gang. In 2002, Connolly was sentenced to 10 years on federal racketeering charges for protecting Bulger and Flemmi, his longtime informants, while they continued a years-long criminal rampage that included dozens of murders. 
 
 Pat Donahue, another woman widowed by Bulger’s mobsters, said the ruling made her “sick to my stomach.” Her husband, Michael, was an innocent bystander who was killed by the gang as he gave a friend a ride home. 
 
 “I can’t understand the legal reasoning behind this,” Donahue said. “It was proven that John Connolly got people murdered. Now they are citing a technicality?” 
 
 Michael Von Zamft, who prosecuted Connolly in Florida, pledged to continue the legal battle to keep him in prison. 
 
 “We plan to file motions seeking a rehearing,” Von Zamft said. “Mr. Connolly presently is right where he belongs, and I guess we’ll do what we can to keep him there.” 
 
 The appellate ruling turned on the prosecution’s decision to charge Connolly with second-degree murder with a firearm, a crime that does not have a statute of limitations in Florida. Without the firearm component, the four-year statute of limitations that existed in 1982 for second-degree murders would have expired by the time Connolly was charged in 2005. 
 
 Brian Kelly, a former federal prosecutor who investigated Bulger’s corrupt relationship with the FBI and helped convict him last year, was blunt when asked what he thought of the appellate decision. 
 
 “Not much,” said Kelly, who now works in private practice at Nixon Peabody LLP. He said he would be disappointed to see Connolly walking free. 
 
 “It would be disheartening, because the evidence at Bulger’s trial, as well as at Connolly’s own trial, was found by different juries to establish that FBI corruption was one of the main reasons that the Bulger group flourished for so long with such devastating consequences to its victims.” Kelly said. 
 
 In the ruling Wednesday, Judge Leslie B. Rothenberg broke from her colleagues and said the evidence supported Connolly’s conviction. 
 
 “Contrary to the majority’s conclusions, the law does not require that the defendant be present or that he commit the last act that caused the defendant’s death,’’ she wrote. 
 
 “It cannot be disputed that the jury found that the defendant carried a firearm during the acts giving rise to his conviction for second-degree murder,” said Rothenberg, a reference to evidence that Connolly wore his service weapon when he met with Bulger, Flemmi, and Martorano in the weeks before Callahan’s murder. 
 
 “It makes no difference whether the defendant had hired . . . a hit man, turned to his mob friends to murder Callahan, or pulled the trigger himself. He is equally guilty,” Rothenberg wrote. 
 
 Steve Davis, 56, of Milton, whose sister Debra was allegedly strangled by Bulger in 1981, assailed the ruling in a phone interview. 
 
 “This whole thing’s been upsetting since the early ’80s when my sister went missing,” said Davis, who was enraged last summer when the Bulger jury returned a “no finding” ruling on his sister’s death. 
 
 “You think it gets better, but it just keeps getting worse. You’re dealing with a government that just doesn’t care.” 
 
 He added of Connolly’s sentence: “Forty years wasn’t enough. There are people getting more time in there for lesser crimes.” 
 
 Peter Mullane, a Cambridge lawyer who represented Connolly in Massachusetts, hailed the appellate ruling. 
 
 “It was a welcome decision, partly for the family and their prospect of finally getting reunited, as they should have been,” Mullane said. “And it was a refreshing decision to read where the court applied the facts to the law, and it was justice finally done.” 
 
 In the seven-week trial, Flemmi testified that Connolly, a decorated FBI agent, took $235,000 in payoffs from him and Bulger and routinely provided them with information, including tips that prompted them to kill Callahan and two FBI informants. 
 
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 Travis Andersen. Kevin Cullen, and Martin Finucane of the Globe staff contributed. MacQuarrie can be reached at brian.macquarrie@globe.com ; Ellement at john.ellement 
 
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– Whitey Bulger's longtime FBI handler might be on the verge of freedom, after an appeals court threw out his murder conviction yesterday. In a 2-1 decision, the Miami judges ruled that because John Connolly Jr. hadn't actually pulled the trigger, he should never have been tried for the 1982 killing of businessman John Callahan, because the statute of limitations for second-degree murder without a firearm had run out by the time prosecutors charged him. Connolly had alerted Bulger that Callahan intended to inform on him to the FBI, prompting Bulger to hire a hit-man, the Boston Globe reports. "It’s interesting that he has a chance to be free," Callahan's widow said. "Unfortunately, my husband doesn’t have that chance." Connolly isn't free yet—the judges sent the case to a lower court "until any and all post-appeal motions are final," denying his lawyer's request for immediate release. Prosecutors do intend to seek a rehearing. "I'm just glad for him that he's finally going to be a free man," one Connolly lawyer tells the Boston Herald. "The only case against John has been out of the mouths of killers." The appeal had been predicted from the moment Connolly was convicted. (Click here for proof.)