The default is if they cause no harm, leave them alone. Indeed, it is a human being s duty to oppose criminal acts regardless of who commits them. Crimes committed in the name of religion are still crimes, and must therefore be denounced. Such conduct remains subject to regulation for the protection of society. Crusaders torturing Jews.
Education is the cure for ignorance.
That education must come from the church or religious individuals themselves, as well as from the community that church resides in. One has no moral or ethical reason to do otherwise. People trust what they know, and distrust that which they are not familiar with. The worse offenders against religious tolerance are members and leaders of competing religions. This is a shame, as those who are religious bigots have failed to understand the fact that to be accepted themselves, they must accept others.