Choices depend on the "rules of the game," and many of those rules are worked out via the legal system. That is as true for religious decisions as it is for other decisions, and the we are witnessing an example of this in the courts right now.
Some church leaders have criticized stay-at-home orders for prohibiting regular religious activities. In fact, this conflict has gone to the courts in Kentucky where a pastor requested that the courts allow religious groups to violate the state's ban on mass gatherings. On Monday, a federal district court denied this request, arguing that the large religious gatherings clearly violate the state ban and that the state ban does not single out religion and so does not violate religious rights. See this short write-up at the Religion Clause blog (the best go-to place on the internet for church-state developments).
A key matter is that religious activities are not singled out. This logic follows a statement issued last week by the U.S. Attorney General William Barr, see here. In essence, it is okay for the government to restrict religious rights in emergencies if religious rights are not being singled out but are only restricted as part of a larger restricting of rights necessary to deal with the emergency.
Of course, these arguments are arguments, and so there may continue to be disagreement. In fact, back in Kentucky, some people continue to challenge the state's ban on gatherings, see here. So far the courts have been consistent in their rulings, which suggests that this latest legal challenge is likely to be unsuccessful.