The December ruling, which drew a national spotlight, came after Schaefer refused a church tribunal's order that he recommit to the discipline or give up his ministry.
But as the public face of church leadership, Johnson took the heat. Hundreds of vitriolic e-mails flooded her inbox.
The attention has faded but not died, even after she declared that she thought her church's laws on homosexuality were discriminatory and that she personally believed sexual orientation was not a choice - just as her blindness is beyond her control.
"A thing we think is broke and not right can often be the very thing that God wants to use for some good purpose," she said in an interview at her Norristown office last week.
During more than 90 minutes, in one of her first extensive interviews since Schaefer's trial, Johnson, 60, was hesitant to let the case and her views on homosexuality define her and take time away from her other missions.
In the same breath, she stressed that continuing to talk about the divide is the only thing that might one day close it.
"I'm not turning my back to the pain," she said. "I want to head straight into it. Let the chips fall where they may."
When Johnson shares a story, she becomes breathless, remembering moments of shock with gasps that send her back in her seat and reliving conversations, only faster. She speaks so passionately that she out of habit grasps at another way to share, her fingers fluttering at her face as she uses sign language to punctuate the occasional phrase.
Johnson learned to sign in her late 20s after seeing a deaf choir perform near her home in Baltimore and being captivated by their billowing white sleeves and expressive faces. They taught her that music had nothing to do with hearing; it's about the soul, she said.
In 1988, she was appointed pastor at the Christ United Methodist Church of the Deaf in Baltimore, the oldest all-deaf congregation in the country. She would end up staying for 20 years, working throughout that time, she said, to translate and advocate for congregants who were denied rights because of their disability.
She likens their fight for passage of the Americans With Disabilities Act in 1990 to the current push for an antidiscrimination law in Pennsylvania, legislation she has publicly supported.
"Just to imagine someone not being able to get an apartment because they're gay just rang my little deaf bells," she said. "Of course you have every right to get an apartment. What's the problem?"
She hasn't always detoured from her church's position on homosexuality.
A group of gay congregants who joined her church in the late 1980s, many who were suffering from AIDS, slowly challenged her beliefs, she said.
While others at the church judged and said that they deserved the disease, Johnson prayed beside hospital beds. When many died, she attended the funerals: one for family members who said only that their loved one had passed from cancer and a second for members of the gay community who mourned deeply for yet another loss.
"I just got aware of this community," she said. "And it sort of transformed me into thinking they were regular people and not monsters."
Schaefer's case became a national story.
He had questioned the church's doctrine since he was in the seminary. His son Tim, who in high school told his parents that he was gay and that he had considered suicide due to confusion over his sexuality, offered him proof that homosexuality is not a choice.
In 2007, Schaefer officiated at Tim's wedding in Massachusetts. He told his superiors but not his congregants at Zion United Methodist Church of Iona, he said.
Then last year, just days before the church's six-year statute of limitations for breaking the discipline was set to expire, a member of his church who had heard about the ceremony filed a complaint with the church's Eastern Pennsylvania Conference.
As the leader of the conference, Johnson played a pivotal role in the ensuing months, trying to negotiate a resolution between the two men.
When one couldn't be reached, she said, she was forced by church law to forward the complaint to a higher office that ultimately charged Schaefer.
Some say she had another choice: to throw out the complaint if she believed it was motivated by a personal grudge.
Johnson said that's not the case and called it "tremendously painful" to be blamed for the trial and its outcome in the letters that flooded her inbox.
"I'm a people person," she said. "To be in a position where I'm perceived as the one who's charging this man and taking away his orders, it's been very difficult."
Since the trial, Johnson has continued to be in the hot seat as some LGBT activists urge her to take a more active role and advocate for changing the church's laws now that she has said they are discriminatory.
Schaefer is among those who say her words are not enough.
"Here are your convictions - you're saying this is discrimination . . . ," said Schaefer, who is appealing the trial verdict. "But you're not doing anything about it. You're the leader. You're the bishop."
Johnson repeats often that she is "bishop to all." She has said she would like the church to be more progressive but cites a long list of obstacles and a belief that the denomination "is big enough that people can find where they're comfortable."
Rather than putting her voice at the forefront, Johnson has stressed that conversations - not to debate but to find common places of connection - have the power to transform opinions.
That's why as much as she would like to move past Schaefer's trial, she is continuing to talk about the experience.
"I'm just nuts," she said, recalling a recent request to talk at a seminary in Washington.
"I [asked them] what do you want? Oh, we want you to talk about the trial. Well, I knew that," she said, letting out a long sigh. "But I'm going to do it. Because I just want to talk."