SAN DIEGO — When Antonio Aaron Bianco arrived for work at his Roman Catholic church office on a recent Monday morning, he was rattled to discover that someone had broken into the conference room and spray-painted a message in large yellow letters on the wall. It said “No Fags.”

For Mr. Bianco, a gay layman in charge of managing St. John the Evangelist Catholic Church, the break-in was just another terrifying omen. Two weeks earlier, someone tried to set the sanctuary doors on fire before the early Sunday Mass. Before that, a stranger swung a punch at Mr. Bianco after Mass one day. For months he had received anonymous phone calls and letters with messages like “Sodomites not welcome in the church.”

Located in the heart of San Diego’s largest gay neighborhood, St. John the Evangelist is one of about 300 Catholic parishes around the country that quietly welcome gay Catholics. Although the Catholic church teaches that same-sex relationships are sinful, growing pockets of the church have accepted openly gay parishioners, staff members and even priests.

But after this summer, when the church faced renewed allegations of clergy sexual abuse, some bishops and conservative Catholic media outlets immediately blamed the crisis on homosexuality. That set off a backlash, fueling a campaign to purge the church of gay clergy members and church workers.