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In his book Political Church, Jonathan Leeman consider the “freedom of conscience” argument as a basis for political freedom. I must admit that I found this argument, compelling and was confirmed in Luther’s words, “To go against conscience is neither right nor safe.” And while I affirm that a well-informed conscience is to be heeded, I also understand that conscience is an insufficient ground to protect the exercise of religion. In Leeman’s words

In short, the traditional liberal formulation simply demands too much for the conscience and too little by way of foundations. Christians will like what it produces only when the vast majority of citizens inhabit a broadly Christian value system. It’s true from a biblical perspective that true worship cannot be coerced, and a biblical perspective on religious tolerance insists on carving out an area for the conscience to freely respond to God, as we will see in subsequent chapters. But this free conscience must remain hemmed in by a concept of right and not just rights. To argue that “the conscience is entitled to remain free” is an overstatement. It invests too much authority in the individual. It presumes too much about the rightness of the conscience’s claim. And in the end it will cave in on itself and undermine true religion because it’s accountable to nothing but the whims of whatever ideologies rule the day. All this is the result of asking the publicly accessible “conscience” to stand in for “religion.” This trade works just fine in a nation of believers and relatively biblically virtuous people. But in a nation of believers and unbelievers, the unattached, unaccountable conscience will be employed to legitimize the freedom of various religions (institutionally defined) only as long as the consciences of a nation’s decision makers value them. When a nation’s decision makers decide that the traditional (substantivist) institutional religions are a threat to liberty or equality or tolerance, they will banish them, first from the public square, then from the marketplace, and perhaps, in partial ways, from the home (“No, you may not indoctrinate your children”).

Leeman, Jonathan. Political Church: The Local Assembly as Embassy of Christ’s Rule (Studies in Christian Doctrine and Scripture) (pp. 90-91). InterVarsity Press. Kindle Edition.