The Crown has said there's no reasonable prospect of a conviction against Albert Rex Baird, in light of the recent Supreme Court decision.
Rhonda Wilson, a mother of three, disappeared in May 2002. Her body has not been found.
Baird, 45, was charged with first-degree murder in May.
Mr. Big operations involve police posing as criminals in an attempt to obtain a confession from a suspect. Until 2008, the tactic had been used at least 350 times to try to solve cold murder cases, the court heard.
The RCMP has said that of the resulting prosecutions, 95 per cent had ended in convictions.
The Supreme Court ruled the Mr. Big technique can induce unreliable confessions.
The ruling places strict limits on how police can use the technique, and a greater burden on the Crown before information obtained in a Mr. Big operation can be used in a trial.
Police would not confirm the exact relationship between Wilson and Baird, but friends of Baird said he was Wilson's common-law husband.
Wilson was 31 years old when she left her Kentville home to go for a walk in August 2002. She was living with Baird and her three children at the time, but was never heard from again.
Police said search crews focused on Bains Road, about one kilometre from an old pig farm in the Annapolis Valley, the focus of weeks of searching last spring.
Wilson's case was added to the major unsolved crimes list in April 2010. Police said they received many tips after that announcement, but they did not contribute to Baird's arrest.
The province said there has been no activity on Wilson's bank accounts since she disappeared.