To add to this, the Catholic Church is not representative of all religious bodies in any way. They are in a unique position, where they are derived from the Roman Empire. They ran entire empires themselves and still directly (in the case of the Vatican) and indirectly run entire countries today. They then used that power to sweep away horrible acts of abuse.
Freedom of religion is an entirely different concept than what the organization of the Catholic Church is.
The issue seems to be more with addressing the power that particular institutions have than the actual religion. That kind of criminal investigation has more in common with going after organizations like the boy scouts than it does with denying freedom of religion.
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