The divisions within the Bay Area’s Catholic community over gay rights hit Marin Catholic High School full force the other day, when a group of nuns walked out of their classes to protest the sponsors of a program intended to protect gay and lesbian teens from bullying.

The five members of the Dominican Sisters of Mary order exited their classrooms Friday as students began handing out flyers at the Kentfield school promoting a nationwide Day of Silence.

Their walkout came one day after 100 prominent local Catholics attracted national attention by taking out a full-page ad in The Chronicle calling on the pope to oust Archbishop Salvatore Cordileone, in part for trying to get teachers at Catholic schools to sign off on a morality clause that characterizes homosexual relations as “gravely evil.”

Marin Catholic High President Tim Navone and Principal Chris Valdez tried to put out the latest brushfire with a letter to parents about “a challenging day on our campus resulting in both students and faculty feeling confused about our mission.”

At issue was Friday’s annual Day of Silence, promoted by the Gay, Lesbian and Straight Education Network — whose corporate sponsors include McDonald’s, Target, Disney/ABC, Wells Fargo, Morgan Stanley, Google and the NBA. It bills itself as a group of “students, parents, and teachers that tries to effect positive change in schools,” but the nuns at Marin Catholic High see it as anti-Catholic.

The school declined to participate in the Day of Silence. Instead, a morning prayer was read over the school’s PA system “to acknowledge and pray for students everywhere who have the experience of being ostracized, marginalized or silenced by bullying,” school officials wrote in their letter.

“Our intention was not to take part in a Day of Silence, but rather take a moment in the morning to pray together as a school community,” the letter to parents said.

Unfortunately, the administrators said, the school’s message was “compromised and misinterpreted” the night before when it was linked on Facebook to the campaign by the Gay, Lesbian and Straight Education Network, “an activist group with which we are not affiliated.’’

When some Marin Catholic High students began handing out Day of Silence-related stickers and flyers on campus Friday morning, the five nuns felt “felt compromised, offended and uncomfortable,” Sister Clare Marie, one of the teachers, later wrote in a lengthy e-mail to her students.

She said the sisters “do not support bigotry or any kind of prejudice,” but that they were compelled to act out against an event promoted by a group that “believes actively in promoting homosexuality in all classrooms, K-12.”

Her e-mail also accused the group’s members of speaking out “against Christians who do not share their views” and handing out materials that “say that any church which teaches homosexuality is sinful is an 'oppressor’ and should be opposed.”

Valdez told us in an interview that the sisters — who make up a small portion of the school’s 60 teachers — stayed away from the campus for the rest of the day, but had informed him of their intentions before they left.

Kari Hudnell, a spokeswoman for the Gay, Lesbian and Straight Education Network, denied that the group “actively promoted” homosexuality in the classroom.

“We are not trying to convert anyone,” she said. “We are just trying to make sure schools are a safe environment for all kids.”

Hudnell pointed out that the group has pushed for antibullying and antidiscrimination laws that apply to religious beliefs, as well as race, gender and sexual orientation.

School officials told parents that the walkout by the five nuns “further confused the students and created some false rumors about the sisters not caring for students who feel bullied, ostracized or marginalized.”

Valdez told us that the school is working hard to cut through the politically charged atmosphere to “bring authentic dialogue to the campus” in hopes of healing any rifts between the students and sisters.