A problem that has been occurring is when a group of people are committing atrocities in the name of a religion to justify their behavior the members of the specific religion, the religious leaders and the followers opposed to the use of their religion to justify the atrocities, should be expected to isolate those in their congregations or those who clothe themselves with the "protection" of the religion, e.g. attending services and recruiting from the congregations, and put them into the hands of those who those animals are slaughtering and mutilating.
When the rank and file of the religion fail to do so, they are in effect "protecting" them.
Rather than wasting time of slicing the bologna thin between blaming a religion for the atrocities and focusing on those who are orchestrating and implementing the atrocities the energy should be spent on digging out the bad guys and ending their reign of terror.
The "freedom of religion" argument doesn't even belong in the discussion, unless one is simply trying to rationalize one's desire to avoid sanitizing the Earth of a spreading cancer, because it is a dirty business. All the "religious freedom" argument does is indirectly legitimize a group of animals who are "animals" from the perspective of the Western culture ...
... the world is outraged by nonlethal waterboarding, but is almost silent to burning alive.