May the Magistrate rightly quarantine and restrain assemblies, including those of the Church, upon sufficient natural and civil warrant?
Rutherford’s answer to that question was ‘Yes’, along with other reformed figures in that era, including the civil government of the Netherlands during the time of the Synod of Dort (1619).
The Reformation, Puritan and presbyterian doctrine, that the Church is subject to the Magistrate in legitimate civil laws and matters circa sacra (around the sacred) is evidenced even in our own day by civil governments (rightly) enforcing fire codes, zoning laws and sound ordinances, etc. upon churches.
See many theological points related to this topic documented from the Reformation and puritan eras, especially from Gillespie and Rutherford, on this new page:
On the Civil Magistrate’s Just Authority for Restraining the Congregating of Citizens, even the Church, and Quarantining, etc., with Sufficient Natural Warrant, according to God’s Moral Law
(The page does not address every issue that ought to be considered in relation to the current response to the Corona virus, such as, what churches should do if the magistrate does not have sufficient natural and moral warrant to forbid their assembly.)