MI6 agent Gareth Williams was vulnerable to blackmail, having carried out unauthorised searches on spy computers, an inquest heard today.
A malign or hostile party could have "theoretically put some pressure on to Gareth", his boss said.
But a Secret Intelligence Services' inquiry ruled out any connection with the discovery of his body in a bag and his "world class" work.
Relatives of the spy walked out of the inquest into his death in tears as MI6 apologised for blunders which saw colleagues fail to raise the alarm about his disappearance for seven days.
The witness, named to the inquest as SIS F, said she was "profoundly sorry" after family lawyer Anthony O'Toole said the agency showed a "total disregard for Gareth's whereabouts and safety".
SIS F blamed Mr Williams' line manager for the "breakdown in communication".
She denied family fears that the "dark arts" of the secret services had been involved in a cover up.
When asked what justification Mr Williams might have had for unauthorised searches, she said: "It seems to me that there was less to this than meets the eye."
She added that a review confirmed there was "no evidence of any specific threat to Gareth and we concluded that there was no reason to think his death was anything to do with his work".
She said Mr Williams was "a fully deployable, highly talented officer" who had passed exams to do some of MI6's toughest covert work six months before he was found dead on August 23 2010.
His examiner said in a report: "I was particularly impressed with Gareth. This was definitely the most intense operational course that I have seen and the improvement needed was immense."
Offering a full apology for MI6's slow response to Mr Williams's disappearance, SIS F said: "We are profoundly sorry about what happened.
"It shouldn't have happened and we recognise that the delay in finding Gareth's body has made it even harder for the family to come to terms with his dreadful death and we are truly sorry for that.
"I also appreciate the delay had some impact on the police investigation."
The spy's non-attendance at work should have been raised as an issue two to four hours after it had been noted, she said.
But measures put in place since his death would "prevent a repeat of what happened," she insisted.
Mr O'Toole blamed the delay for preventing the family from saying goodbye to Mr Williams while his body was in an "acceptable form" and for making it more or less impossible for detectives to establish how he died.
"Because of the decomposition of the body, any forensic evidence that could have been derived from it has disappeared, so the police investigation has in essence been almost defeated," he said.
When officers finally entered Mr Williams's flat in Pimlico, central London, they discovered among his possessions some £20,000 of high-end women's clothing and shoes.
Examination of his home computer showed he had also visited websites about claustrophilia - the love of enclosure - and bondage and sadomasochism, the inquest has heard.
Mr O'Toole told the witness of speculation "that revelations about Gareth's private life might have rendered him unsuitable for SIS work".
She replied that it was a "sensitive area" of questioning as it related to vetting issues but indicated his lifestyle and sexual preferences would not in themselves have posed a problem.
"I can't respond directly to the questions over Gareth because that goes to what knowledge we did or didn't have of him," she said.
"There's no set template as to what (an employee's) lifestyle should be. Individuals have lifestyles and sexual choices which are perfectly legitimate.
"Our concern in the vetting process is to identify whether anything in the individual's background, lifestyle, creates a risk for him."
But she stressed it was helpful for an employee to discuss any lifestyle issues with SIS so they could make a decision as to whether these might pose any risk.
Mr Williams was on secondment to MI6 in London from GCHQ before he died but had asked to cut this short, in part because he was disillusioned with the bureaucracy there, Westminster Coroner's Court has heard.
It was "quite rare" for someone to request an early termination of their secondment but the spy had seemed happier once his request had been accepted, SIS F said.
Yet before his planned departure from London could happen, his naked body was discovered curled up in a padlocked hold-all in his bathtub.
Some 20 months on, the circumstances of his death remain shrouded in mystery.