If the wording of the local county statute applies generally to EVERYONE then there is no violation of the Establishment Clause of the Constitution.
That is only one element they might weigh so in broad terms you are mistaken. Hypothetically, they may write a law saying no one may have a large cross attached to a building or structure, which may apply generally to grocery stores, residences, and the barber shops as well as Christian Churches but no court will be fooled if they suspect the 1. there is no secular purpose to the statute because other shapes are allowed and that big fat McDonalds golden arch on Fifth and Main is doing just fine! 2. its primary effect is to inhibit a religion, because nobody else tends to have large crosses on the their buildings while 6 local churches have to take theirs down. I mean they aren't stupid! That is why the lemon test was put in place. They are looking holistically at everything from legislative intent to ultimate impact. If you mean in this case, I agree with you that these quarantine measures absolutely pass the Lemon Test including the one you are applying.