The situation in Maaloula underscores the core problems that bedevil the movement against Mr. Assad: the opposition, rooted in Syria’s Sunni majority, has failed to win over enough Christians, who make up 8 percent to 10 percent of the population, or other religious minorities. More than 450,000 Christians have fled their homes, church leaders say, during more than two years of war.

On the battlefield, well-armed radical Islamist groups, including foreign fighters, show little inclination to coordinate with local battalions, and sectarian killings and references to non-Muslims as infidels further intimidate Christians. In Maaloula, according to fighters, the rebel attack was led by members of the Nusra Front, a group with ties to Al Qaeda in Iraq, even after local fighters affiliated with the Western-backed Free Syrian Army tried and failed to dissuade them.

Last week, as the battle began, opponents of American military action in Syria circulated a recent video of a Syrian Christian woman accosting Senator John McCain, a proponent of military action, accusing him of abandoning Christians. “I could trace my family’s name to the Bible,” she said. “We refuse to be forced to leave.”

Maaloula has long symbolized Syria’s history of diversity and coexistence. Legend has it that as an early Christian saint, Taqla, was fleeing persecution, the cliffs parted to help her escape, giving the town its name, which means entrance in Aramaic. More recent lore says a small Sunni population sprang up after a Christian man converted to marry a Muslim.

Even after a movement for political rights morphed into a civil war, local Sunni and Christian leaders worked to maintain calm. Local groups of rebels have long occupied the Safir hotel on the edge of town. But until last week, Mother Sayaf said, residents moved unmolested between rebel and government territory.