Good thoughts. I think we need to distinguish between the most prudent courses a voting citizen or lesser magistrate may take in an effectively heathen nation to preserve the liberty of true worship from the unbending responsibility of a government before the Law of God.
In the US, the ability for the magistrate (even the President) to punish heresy is minimal and would require a Constitutional amendment to enable which could not happen absent a massive national revival--something we can certainly pray for but which does not appear to be happening at present. Therefore, citizens and magistrates must seek to protect the church, as the US revisions say, and if some believe that it's through a modified libertarianism, that's a matter of prudence and not dogma. The Scriptures do not indicate that Joseph or Daniel attempted or were to attempt prosecution of heathens in (civic) rebellion against their superiors from their positions in foreign kingdoms.
When a nation is governed by Christians who have the ability to determine the laws of the land, however, I do not see how one could escape the conclusions of the original Westminster confession. Heresy is not merely an ecclesial issue, it is rot and moth to the fabric of society. Does rampant theft harm a nation? Heresy does more. Does dishonesty harm a nation? Heresy does more. If, according to Paul, a magistrate in his proper role is a revenger to execute wrath on him that doeth evil, is that to except the false prophets of heresy and peddlers of idols? Even in the US we at least had laws to prosecute violations of part of the first table in the Sabbath laws at one point.