An industrial tribunal this week dismissed allegations of constructive dismissal brought by John Woodward against Nisa, which he had worked for as a business development manager.
Following the ruling, Nisa accused the Nisa Members Association, a group of shareholders that publicly opposed the merger, of using Woodward as "a pawn".
"The tribunal rejected all of John Woodward's allegations," said a statement from the buying group.
"It came to a unanimous decision that the claimant was fairly dismissed, that he has not been subjected to a detriment, there were no damages for breach of contract and the company had not made an unauthorised deduction from Mr Woodward's wages.
"It was also found that the NMA were a highly organised partisan group seeking to oppose the company and Mr Woodward was a pawn in their strategy to seek publicity for their own ends when he wrote the letter to Nisa-Today's."
Woodward became embroiled in a row with his employer in 2006 when a letter he wrote to the board that accused Nisa and Costcutter of being involved in cartel behaviour was leaked to the press.
The letter claimed Nisa had ignored applications from Costcutter franchisees who wanted to become members because the board feared they would vote against the merger.
The accusations led to an investigation by the OFT that dragged on long enough to scupper the merger, even though both companies were eventually cleared of the allegations.
Nisa is believed to have spent tens of thousands of pounds on legal fees defending itself against the accusations, while high profile figures such as CEO Neil Turton gave evidence at the hearing. It is understood that Woodward is considering an appeal.