FreeBYU, a group of former students and others pushing for Mormons to be allowed to leave the religion but stay in school, notified Juergensmeyer and other scheduled speakers of the policy last week.
"It's kind of a weird non sequitur," said group spokesman and BYU graduate Caleb Chamberlain, "to be a proponent of religious freedom but to deny it to your students."
FreeBYU maintains that if students resign from The Church of Jesus Christ of Latter-day Saints, they should be allowed to obtain an "ecclesiastical endorsement" from the BYU chaplain or their new religious leader and pay the non-LDS tuition to remain in school.
Juergensmeyer, director of the Orfalea Center for Global and International Studies at UCSB, was the only scheduled speaker to call off an appearance, said Elizabeth Clark, associate director of BYU's International Center for Law and Religion Studies.
"What can I say? We respect his point of view," she said. "We support the right of all individuals to honor their conscience."
Clark offered a different view on the university policy Tuesday. Religious freedom extends to faith-based institutions, she said, which have the right to determine their membership requirements.
"We respect that, whether it's LDS, or Catholic or Muslim," Clark said. "That's an important part of religious freedom."
BYU spokeswoman Carri Jenkins in a statement acknowledged that Mormons who change faiths are treated differently than those who begin their first semester as non-LDS.
The university "is very open and clear about its mission as a religious institution," Jenkins wrote.
The school stresses that the rule applies to students who leave the LDS Church and not students who struggle with faith issues for a short time. Employees work with students questioning their faith on a case-by-case basis.
The BYU website detailing its honor code makes it clear for Mormon students:
"Because of covenants and commitments members of the LDS Church have made," it reads, "they can no longer remain in good honor code standing if they chose to formally disaffiliate from the LDS Church." Disaffiliation, as stipulated by the policy, means a removal of a person's name from church official records.
Non-LDS students pay double what a Mormon student does at BYU on the basis that LDS families help support the faith's flagship school through their tithing. Full-time LDS undergraduates pay about $2,500 a semester, while non-Mormons pay $5,000.
For his part, Juergensmeyer said he believes it would be hypocritical to participate in a religious liberty gathering hosted by an institution that "fundamentally violates this principle."
His decision is "an act of conscience," he said, echoing a letter he sent to symposium organizers over the weekend.