Six points of consideration, then a conclusion:
1. The US does not give govt' money to churches. It merely refuses to tax them. There is a difference. And doing away with this entirely might be the best course of action due to the abuses involved.
2. Laws reflect morality and the 10 commandments are moral. Therefore, the Sabbath laws in the past served to close stores, etc, so that people could worship, but stopped short of demanding coerced church attendance. There is also a difference there as well. The first was promoting general morality, the second was to levy the civil sword to enforce ecclesiastical affairs.
Some could counter-argue and insist that the government could also enforce church attendance of some type without specifying the specific church, as long as they went somewhere for mandatory worship on Sundays. But even this is too far, I believe, for then you'd have to register approved churches to prove that you attended an actual church. And this is what happened in the past.
3. Baptist were persecuted in both Europe and then again in America under such systems. In years past many on the PB always scoff at that and say, "Naw....we'd NEVER do that. Baptist are silly for even bringing this point up." And maybe baptists are now too numerous to make easy victims. But it happened in the past. Twice. And it happened because of the mixture of church and state.
Here is an example of how this happened:
"Early Baptists did face opposition. Dozens of their ministers were jailed before the American Revolution. Some, particularly among the Separates, had refused to obtain legally required preaching licenses. Others violated the terms of their licenses, which usually specified places of worship, making itinerancy and revival meetings illegal. Some were incarcerated for the more general charge of disturbing the peace. Both preachers and congregants also sometimes ran afoul of the local churchwardens, as all Virginians were legally required to tithe to the Anglican Church and attend Anglican worship at least once a month." https://www.encyclopediavirginia.org/Baptists_in_Colonial_Virginia#start_entry
4. Historically we see every time the State prefers the Church, that the Church sinks into error from that point on (medieval Europe after Constantine). When persecution or toleration turns to support in the form of the State getting involved in "helping" the Church, the Church always suffers from the taint of the State's touch.
[cue the meme of Ralphie Wiggums from the Simpsons saying, "I'm helping!" That is the State "helping" the Church].
Power corrupts. And it corrupts religious institutions who think they are doing the will of God, too. Sometimes even worse.
The Anglicans persecuted the baptists and were the State-Supported established Church in the Colonies. But where are the Anglicans in Virginia now compared with the baptists? The State Churches in Europe now are dead mostly. But the Gospel is still alive in America.
The "help" of the State was poison to the Church in the long-run.
5. Back to the OP, discipline in Calvin's Geneva was repressive. He meant well and he was reforming. But let's be real and admit that he went overboard sometimes. The Gospel is strong enough that it does not need the puny arm of civil fines and punishments to protect it.
6. The govt' is largely spoken of in the negative in the NT. We run to Romans 13 because our government has not yet turned on us, but we forget about Revelation 13. Big Government is Beastly.
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I mean, does any Presbyterian today really believe the current US government has the power to call and preside over synods? Do we expect or want President Trump (as much as I like him...MAGA y'all!) to preside over the next Nicene Council?
The larger idea here is that the concept of "Christendom" has died. That is hard to swallow, but I believe it to be a good thing. Calvin was still operating under the "Christendom" concept of the faith. We no longer have such a thing.
Finally,
Call me a hopeless American, but I really believe that the Establishment Clause is much better written than the theocratic parts of the original WCF before the 1788 American Revision.
"...no man shall be compelled to frequent or support any religious worship, place, or ministry whatsoever. . . nor shall otherwise suffer, on account of his religious opinions or belief; but that all men shall be free to profess, and by argument to maintain, their opinions in matters of religion.”