He refused to voluntarily surrender his credentials when asked by the board president.
"To which she said, 'Well, we're taking them.' And that was the end of it." Schaefer said.
Later, he said, "I said to myself, 'You know, I just can't see them taking my credentials.' I mean what I did was an act of love for my son. And they did anyhow."
Although the Methodist church accepts gay and lesbian members, it rejects the practice of homosexuality as "incompatible with Christian teaching" and bars clergy from performing same-sex unions.
The issue has split the nation's largest mainline Protestant denomination amid a rapid shift in public opinion. Same-sex marriage will soon be legal in 16 states, and opinion polls show that a majority of Americans now support it. Hundreds of Methodist ministers have publicly rejected church doctrine on homosexuality, and some of them face discipline for presiding over same-sex unions. Last month, in a public challenge to church rules, a retired Methodist bishop officiated at a wedding for two men in Alabama.
Most other Protestant denominations have decided their position on the issue one way or another. But the Methodists, with about 7.7 million members in the U.S. and many more members overseas, remain divided. At their last national meeting in 2012, delegates reaffirmed the church's 40-year-old policy on gays.
Associated Press writer Michael Rubinkam and AP Religion Writer Rachel Zoll contributed to this report.