The Sun's executive editor Fergus Shanahan, 60, said despite the acquittal of four journalists at the Old Bailey their families had been through a "terrible ordeal".
After hugging supporters outside court, Mr Shanahan said: "Obviously I'm very grateful to the jury for taking such time over the verdict. They put an enormous amount of thought into it."
He said the issues that the jurors in the case had to deal with were complicated and "complex".
The executive editor told reporters that the trial had been a "terrible ordeal" for the families of the people involved.
While journalists may have "thick skin" and "can look after ourselves", the loved ones had been put under "the most appalling strain for three years", he said.
The journalist added that his thoughts were with colleagues facing trial in the future and he expressed the hope that there would be a "sensible result, a right result".
Sun chief reporter John Kay - one of four journalists acquitted at the Old Bailey - said he was "very, very upset" a trusted source of the Sun newspaper had been jailed.
Thanking family and friends who stood by him Mr Kay, 71, said: "It's a great relief that a three-year ordeal is over.
"I just hope that this result bears fruit for other colleagues in a similar predicament."
Asked about his source Bettina Jordan-Barber, who was jailed for a year after pleading guilty, he said: "I'm very, very upset that a trusted source of the Sun ended up in jail as a result of betrayal by my own company."
Calls for a "witch hunt" against newspaper journalists to end came amid emotional scenes outside court when four senior Sun journalists were cleared of wrongdoing over payments to public officials for stories.
I'm not going to say much but 1,060 days ago eight policemen raided my house at six in the morning.
There is no celebration while this witch hunt continues against my colleagues who are still facing the nightmare that I hopefully one day will wake up from.
Royal editor Duncan Larcombe appeared tearful as he left the Old Bailey with his arm around his wife who had supported him throughout the trial. Asked if he thought charges against other journalists should be dropped, he said: "Of course I think that, but this is all I'm really allowed to say." The 39-year-old journalist said he was "just relieved" at the verdict.
Four senior journalists from The Sun, including chief reporter John Kay and royal editor Duncan Larcombe, have been cleared at the Old Bailey of paying public officials for stories.
Kay, 71, and Larcombe, 39, were found not guilty of wrongdoing over their contact with two military sources between 2004 and 2012.
The Sun's executive editor Fergus Shanahan, 60, and deputy editor Geoff Webster, 55, were also cleared over allegations that they signed off payments.
All the defendants had denied the charges against them.
Liverpool Labour councillor has resigned from the party in protest at Ed Miliband’s support for The Sun newspaper.
Cllr Martin Cummins, who represents Croxteth, told the Liverpool Echo that the Labour leader's picture holding up The Sun newspaper had “rocked me to my core”
His resignation letter said:
We are the the party of truth, justice and equality and we must stop compromising on our moral foundation just to win votes.
It is therefore with sadness and sincere regret that I am resigning from the Labour Party.
I pray that my brothers and sisters within our Labour family will understand my decision.
Ed Miliband has apologised after posing with a copy of The Sun, distributed for free in Liverpool to mark the start of the World Cup.
Labour figures in the city expressed anger at his action for failing to take account of continuing fury over the tabloid's coverage of the Hillsborough disaster.
"Ed Miliband was promoting England's bid to win the World Cup and is proud to do so," a spokesman for the party leader said.
"But he understands the anger that is felt towards The Sun over Hillsborough by many people and he is sorry to those who feel offended."
The Sun's Political Editor Tom Newton Dunn, who broke the original 'plebgate' story, has claimed the police officer's admission today to falsifying witnessing the row, was merely "a red herring to the main event": the Downing Street PC who alleged Andrew Mitchell called him a "pleb".
Worth remembering Keith Wallis's part in #Plebgate came a day after the row at gates. So a red herring to main event; if Mitchell said pleb.
Also worth remembering PC Toby Rowland, who made 'pleb' allegation, has been fully vindicated by Met/CPS/IPCC, + he is still suing Mitchell.
A Sun spokesman said: "We stand by our story and will defend Mr Mitchell's claim vigorously".
Mr Mitchell is suing the paper for libel.
In a statement, he said: "I am pleased that justice has been done in a criminal court today....I am looking forward to seeing justice done in the up to 10 other related disciplinary cases involving police officers"
The Associate Editor of The Sun Trevor Kavanagh has accused politicians of taking the press to the "brink of political control", a move he claims is a "bridge too far".
The final decision to reject the newspaper industry's plans for regulation is expected to be announced by Culture Secretary Maria Miller in the Commons later today.
Mr Kavanagh insisted three centuries of press freedom needed to be protected, before suggesting that a future government may decide the press is too free and enforce further restrictions and regulation.
Commenting on reports ministers have rejected plans drawn up by the newspaper industry for press regulation, Trevor Kavanagh, the associate editor of the Sun, told Newsnight it is not a shock.
He added: "It's what we'd been given fairly clear clues would happen. I think it has to be seen as a great victory for the forces of oppression of a free press - Hacked Off in particular - and the politicians who went along for the ride."
The Irish Sun has dropped its topless page three pin-ups, saying it "caters for a different audience" to the UK edition which is keeping the long-running feature.
The paper's editor Paul Clarkson said: "The Irish Sun shares the same qualities and personality that make the paper great everywhere: entertaining and engaging journalism, quality sports writing and showbiz coverage.
"But it also caters for a different audience in Ireland and we always strive to reflect our cultural differences here."