Stetser praised Winters for her "amazing contributions" to the school.
"In the Mercy spirit, many of us accept life choices that contradict current Church teachings," she wrote, "but to continue as a Catholic school, Waldron Mercy must comply with those teachings."
Winters married her wife in Boston in 2007, seven years before a federal judge struck down as unconstitutional Pennsylvania's 18-year-old law banning gay marriage.
The Supreme Court on June 26, in a 5-4 ruling, said same-sex marriage is a constitutional right.
Winters said she and her wife "kept a really low profile" about their relationship at the school.
"I actually had a conversation with the principal a few weeks after I was hired to say, how should I handle this," said Winters, adding that she was advised that she could be open about her life with the faculty but to avoid discussing it with students' parents.
"So that's what I've done," she said. "I've never been open. And that's been hard."
Still, parents of at least two students discovered that Winters was in a same-sex marriage. Winters said one complained to the school and the other contacted the Archdiocese of Philadelphia.
Winters refused a request to resign and was fired in a June 22 letter from the school.
Winters said she thought the school's connection to the archdiocese played a role in that decision. The school, she said, worried that its "Catholic identity would be in jeopardy."
Stetser said in a statement that she could not discuss personnel matters.
"The primary consideration that guided my decision-making process was to sustain the Catholic identity of Waldron Mercy Academy," Stetser said.
Ken Gavin, director of communications for the archdiocese, said it played no role in Winters' firing. "There has been no discussion whatsoever about revoking the ability of the school to identify itself as Catholic," Gavin said.
Winters' firing comes 11 weeks before Pope Francis visits Philadelphia for the World Meeting of Families, a Catholic gathering expected to draw 1.5 million people.
The weeklong event is to include a discussion of sexual orientation. The recent Supreme Court ruling on gay marriage is also expected to be discussed.
Archbishop Charles J. Chaput, in a weekly column released Monday, called that ruling an "abuse of judicial power" with huge implications.
"And the last thing we need from religious - including Catholic - leaders in the face of this profoundly flawed Supreme Court decision is weakness or ambiguity," Chaput wrote.
Lower Merion Township has an antidiscrimination ordinance that protects employees for several reasons, including sexual orientation. Religious institutions are exempt unless they are "supported in whole or in part by government appropriations."
State Sen. Daylin Leach, a Democrat who represents the school's area, noted that Waldron Mercy lists on its website that it has received more than $270,000 in the last two years from the state's Opportunity Scholarship Tax Credit program.
Waldron's website also said 70 students have attended since 2005 under a similar state program, the Educational Improvement Tax Credit.
"So they've received a good bit of money from the State of Pennsylvania," said Leach, a lawyer. He said that state money might override the religious exemption for the township ordinance.
Stetser wrote in her e-mail that she wanted the controversy to lead to conversation and then clarity.
"My hope is the pain we experience today adds to the urgency of engaging in an open and honest discussion about this and other divisive issues at the intersection of our society and our Church," she wrote.
The conversation is certainly coming, according to some Waldron parents.
Nancy Houston and her husband plan to host a parents' meeting Wednesday evening.
"It was a surprise, coming from Waldron," Houston said. "That's not who we are. Right now, there's a lot of questions."
The firing, she added, is "not something we're going to accept quietly."
Winters "makes kids love religion," Houston said. "She's a perfect example of living a religious life."
Winters said she welcomes the attention.
"People of faith need to know what is happening in the name of their church," she said.