The congregants lined up 6 feet apart on Palm Sunday, waiting to take communion at Godspeak Calvary Chapel in Thousand Oaks. Ten people were allowed inside at a time, with someone spraying chairs with disinfectant after each use.

By the end of the day, hundreds of people had cycled through.

Nearby, in the church parking lot, protesters lined up their cars and honked their horns, disturbed that the church would so brazenly flout stay-at-home orders from Ventura County and the state, put in place to battle the coronavirus pandemic.

It wasn’t a decision Pastor Rob McCoy took lightly. On Saturday night, he resigned his position on the Thousand Oaks City Council, saying he planned to violate orders that deem churches nonessential.

"As an elected official I am in conflict and thus must tender my resignation from the council," he wrote in a letter obtained by the Los Angeles Times. "I have no desire to put our community at risk and will not. ... However this is portrayed, please know I am obligated to do this."

As the novel coronavirus continues to spread, pastors such as McCoy have revolted against stay-at-home orders, pitting public health concerns against claims of religious freedom.

And houses of worship have already proved to be hospitable breeding grounds for the virus, which as of Sunday had killed at least 347 California residents. Bethany Slavic Missionary Church in the Sacramento suburb of Rancho Cordova became the epicenter of an outbreak when more than six dozen of its members tested positive for COVID-19.

The Pentecostal church stopped holding large gatherings March 18, according to its website. But public health officials last week worried that church members were still meeting in private homes to conduct services.

“It’s outrageous that this is happening,” said Dr. Peter Beilenson, the Sacramento County public health director. “Obviously there is freedom of religion, but when it’s impacting public health as this is, we have to enforce social distancing.”

In his resignation letter, McCoy detailed the church’s efforts to keep its members safe. Though the church can seat 400 people, congregants who wished to take communion on Sunday afternoon would cycle through 10 at a time during a two-hour period after a morning livestreamed service.

Those who didn’t want to step inside the church drove up behind it to take communion. Youth director Elijah Swartz, 22, served plastic cups of wine and bread from a wooden plate attached to a long pole. After each visit, he cleaned the plate with a Clorox wipe. He wore a mask and plastic gloves.

“They were taking a lot of precautions to make sure everybody was safe,” said Robyn Freeman, 39, a Tustin resident who went to take communion with her mother, who lives in Westlake Village.

She said the criticism of the church was unnecessary, noting there were signs inside advising congregants not to hug or touch one another.

She was grateful for the opportunity to pray.

"I just prayed for our world, just that this epidemic, this pandemic, would cease soon," she said.

Noel Hazard, 63, showed up to express his displeasure with the event, which worried him because it was attended by members of his own community.

“They shop at the same stores we do, the same pharmacies, go to the same gas stations,” he said. “There is a risk.”

Thousand Oaks Mayor Al Adam said McCoy, who has served on the council since 2015, was a “voice of strength and healing” after the city endured back-to-back tragedies: the shooting at the Borderline Bar & Grill and the Woolsey fire.

“He recognizes the fact that he has a calling here that is in conflict with his duties as a City Council member, so to his credit he resigned,” Adam added. “I think it was the right thing to do.”

Cross Culture Christian Center, a small evangelical church in Lodi, also continued to hold services despite stay-at-home orders. The pastor intended to convene Sunday, despite San Joaquin County health officials ordering the building closed.

“We’re going to meet as often as we can meet, and we do believe that this right is protected by the First Amendment and should be considered essential,” the church’s pastor, Jon Duncan, said in an interview with Fox 40 News last week.

But on Sunday, Duncan was greeted by several police officers in the parking lot about an hour before he planned to hold an in-person service.

Duncan’s church leases space in Bethel Open Bible Church, which stopped hosting in-person services March 15. Bethel changed the locks on the building to prevent Duncan and his congregants from entering, Lodi Police Lt. Michael Manetti told the Times.

On March 25, Lodi police officers came to one of Duncan’s Wednesday services and told the pastor about county and state orders against public meetings.

In response, the church retained a lawyer from the Escondido-based National Center for Law & Policy, a conservative Christian nonprofit law center.

Attorney Dean R. Broyles sent a six-page cease-and-desist letter to the city of Lodi, saying officers had “disrupted a peaceful and lawful worship service” and demanding that the city respect the church’s First Amendment rights.

“The church intends to meet this Sunday, and all future Wednesdays and Sundays in the future,” the March 27 letter said, noting the church has implemented social distancing measures and has asked the elderly, sick and those with compromised immune systems to “stay at home.”

On Friday, police officers posted a notice from county health officials on the church building. The letter, addressed to the pastor of Bethel Open Bible Church, said Cross Culture Christian Center was continuing to hold services at the facility and ordered it and its parking lot closed.

Violation of the emergency order, the letter said, was a misdemeanor punishable by fine or imprisonment.

In an interview with the Times, Broyles said he planned to send a letter Monday to Gov. Gavin Newsom and San Joaquin County officials asking that they follow the lead of some other states and declare houses of worship as essential services exempt from stay-at-home orders.

Broyles said he is also planning a federal civil rights lawsuit “based on the fact that the governor and the county are violating my client’s First Amendment rights.”

The church, which has 60 to 80 attendees on a regular Sunday, believes the Bible calls for churches to meet together, in person. And, as of Sunday, Broyles said, no congregants had gotten sick.

“There’s a lot of things the Bible commands us to do, like love one another, serve one another, encourage one another,” Broyles said. “And those are difficult to do, if not impossible, if you’re not together.”