Martin Davis said the Watchtower Society should return the money left to it by his cousin Donald Kennett so it could go to Kennett's nephew, who is autistic.
Accepting money from a member who had been expelled would damage the charity's reputation, said Davis, of Dulwich, south London.
Kennett was befriended by a Jehovah's Witness in the 80s when recovering from a serious car crash and joined shortly afterwards, Davis told Third Sector. He was 'disfellowshipped' from his group in Stockport in 2001 after members discovered that he was contacting call girls.
When Kennett's mother died in 1994, she had left half her estate to him and half to his autistic nephew. Kennett's own will left all of the resulting £100,000 to the Watchtower Society.
Davis said he acknowledged that the charity had a legal right to the money but argued that it should return it on moral grounds and to prevent damage to the charity's reputation.
"The society should not wrongfully gain the reputation of putting its financial interests before its moral obligations," he said. "It expelled Donald as if he were polluted or unclean. It should have refused the money. It's as simple as that."
A Charity Commission spokeswoman said it had advised the Watchtower Society that trustees have a legal obligation to use funds for the charity's cause, but that they can seek permission to make an ex-gratia payment if it is in the best interests of the charity.
"We would need to be satisfied that the trustees believed themselves to be under a moral obligation to make the payment, and we would need to see the grounds on which the decision had been made," she said.
The Watchtower Society wrote to Davis saying it did not think the commission would permit it to make an ex-gratia payment and informed him that it intended to close the case.
Davis said the Watchtower Society did not refer to a moral obligation in its letter to the Charity Commission. "If no such case was made to the commission, it would feel no duty to permit a payment," he said. "But if a moral case to relinquish the estate was advocated, the Charity Commission would be unlikely to reject it."
A spokesman for the Watchtower Society said: "The trustees sought guidance from the commission and, after considering Davis's submission in light of the advice, concluded that a payment would not be permitted."