It seems what you take issue with is the definition of "essential". That's fine: but even if California is allowing businesses that are not truly essential to remain open, that doesn't change whether or not Churches are essential. A mistake by California in one are does not require that it apply the mistake elsewhere. And again: every type of gathering style similar to what would be experiences in churches has also be put on hold. Are you aware of any business that has a similar exposure profile as churches, and is not necessary for normal everyday survival (food etc.) that has been allowed to remain open? (Though even if you are, again such a mistake by California does not require it to double down on that mistake with other such gatherings.)
And indeed, under this current order, they haven't.
They've limited them to min(25% capacity, 100). What's under contention is whether this is treating churches differently than other similarly-situated secular facilities. The two sides come to a disagreement over which other facilities count as "similarly-situated".