A US government does not get to tell people how to practice religion beyond making a determination whether the belief system is a religion. And, making a determination if a particular practice is legal (to exclude harms like you mention).

That is why I have been careful to describe protected religious practices using the term 'otherwise lawful religious practice'.

The plaintiffs clearly practice a religion. Going to church is clearly a legal religious practice. Thus, the government needs to prove that shorter lines at grocery stores are more important than longer lines or less capacity at churches. The government can't prove that because it can't interpret (or weigh) the importance of going to church.