Mr Doherty was laid to rest after Requiem Mass at Long Tower in Derry
Hundreds of mourners have attended funeral of Kieran Doherty, who was murdered by the Real IRA on Wednesday.
The body of the 31-year-old was found naked and bound on the Braehead Road on the outskirts of Londonderry, near the Irish border on Wednesday.
The Real IRA said it killed Mr Doherty, who was one of its members.
Father Roland Colhoun, who celebrated Requiem Mass at Long Tower in Derry, condemned those responsible for Mr Doherty's death.
"To those who killed Kieran, I think we should say that they have brought terrible distress to his family.
"In the decisions you made last Wednesday, you changed the lives of his family.
"You too have humanity in you. Could you not have appealed to the goodness within you to see the goodness within Kieran. Did you have to take his life?"
His family have called on the First and Deputy First Ministers to investigate whether MI5 had tried to recruit him as an informer.
In the Assembly on Monday, Foyle MP Mark Durkan said MI5 have "serious questions to answer" over their activities in the final months of Mr Doherty's life.
Mr Doherty was found shot dead on Wednesday night
He also said it was important the house demonstrate its unity "in rejecting those who would seek to use violence in the name of any cause".
"It is important we reject the pretensions of those who believe they can act as judge, jury and executioner over anyone, and who pretend they act in the name of our country and who pretend they are pursuing some pure cause with these deadly means."
East Londonderry DUP MP Gregory Campbell said his thoughts and prayers were with the Doherty family, and called for those responsible to be brought to justice.
"Information is vital, and information needs to be given to the police so that the guilty are caught and to ensure these days will remain in the dim, distant and painful past."
Sinn Fein assembly member Martina Anderson also urged anyone with information to come forward.
"I have spoken to Kieran's family over the weekend, and they want justice to be sought for his murder.
"We are also seeking answers to the link between MI5 and this group calling themselves the Real IRA, as it is generally believed that this organisation is not only infiltrated by MI5 but also by criminals, and their activities are anathema to Irish republicanism," she said.
UUP assembly member Basil McCrea offered his condolences to Mr Doherty's family on behalf of the party.
"The people of Northern Ireland have a choice," he said.
"They can either look forward to the rule of law and order and peaceful coexistence, or risk going back to the bad old days."
Mr Doherty's mother Christine said the way her son died was "brutal".
"They threw him in the road like a dog and brutally murdered him," Christine Doherty said.
"They stripped him, tied him up and brutally shot him twice in the head - they gave us a reason, something about a criminal gang, which is the first time I've ever heard of it."
On Friday, his family said that he had been the subject of "continuous harassment" by MI5 and that the security service had been trying to recruit him as an informer.
The family have admitted that he had been in jail but claimed he had been "trying to get on with his life" since then.
The family statement added: "Kieran was a good and decent man trying to lead a normal life and looking forward to getting married."
They said in the last months of his life he was stressed, lost weight, was treated in hospital for depression and was sometimes almost unable to speak to his partner.
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