Again, the first Amendment limits the powers of Congress, i.e. the Federal government. It says nothing about state governments. Several states had established churches for many years after the adoption the the Bill of Rights. Courts have since ruled that the states are bound by some of the rights guaranteed by the Bill of Rights*. I seriously doubt that courts have ruled to limit states’ powers regarding assembly during times of emergencies.
* It wasn’t until June of 2010 that SCOTUS said that states were obliged to follow the 2nd Amendment even though the 2nd does not use the language “Congress shall not...” but the much more direct “...shall not be infringed”.
It’s a slippery slope, and I do not like it one bit. Your rights are being denied, whether you know it or not.