At some point pogroms occur.
A pogrom (from Russian, “violent destruction”) is a mob activity where the targeted place of business or institution is trashed. The violence may or may not extend to physical harm done to the people associated with the target of the pogrom. The pogrom activity is supposed to appear as spontaneous outrage, however often it is organized or encouraged in a way that the organizer can deny responsibility. The government may distance itself from those committing the pogrom or even condemn it, however it will not take a meaningful police action to limit or prevent the pogrom from happening.
The pogroms originated in Tsarist Russia as a reaction against Jewish revolutionaries convicted of terrorism. The targets of pogroms were Jewish businesses hardly connected to the terrorists other than by nationality. A similar wave of violence went through Germany in 1930s; the Kristallnacht — the Night of Broken Shop Windows is better known. Both Muslim and Christian sides in the Kosovo conflict were accused of pogroms on recent history. Violence by sundry anarchists and left wing progressives that erupts during international summits and targets banks and other businesses is another example of recent pogroms.
A defense against a pogrom is advance request for police presence, but that requires more than nominal cooperation from the local government. A community expecting a pogrom should organize and get educated on how to minimize confrontation. A trained volunteer self-defense force is probably a good idea. Any form of community defense should recognize the fact that any armed action will be interpreted by government courts as provocative, excessive or outright offensive, and arm and train accordingly. Fortunately, the ubiquity of portable cameras makes legal defense easier, so film all action that you witness and stay in groups.
"The city was left vandalized, subjected, and violated. If they had done it to a synagogue, it would have been said that it was an anti-Semitic aggression. As it was against Catholics, there’s no problem"
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In 2010 they vandalized buildings in the city of Paraná [Argentina], attacked Catholics in front of the city’s cathedral and seriously injured at least one person. Similar confrontations have occurred in other years as well, including 2007 and 2008.
Video: Catholics assaulted, spat upon, and spray-painted as they defend cathedral from feminists
Of course, in the Muslim world violence against Catholics and other Christian is not new: churches are trashed and firebombed routinely. We should not expect a better behavior from atheists, who, after all, do not have a moral constraint that a Muslim would at times have.