For what it's worth, my understanding of the origins and intent to not call a religious use an "E" occupancy, goes back to the original intention of "Sunday School", where the parents we in a church service in the sanctuary, while the kids were in "sunday school class" in other rooms on the same campus.
If there was a fire or other emergency, the parents could go to the classrooms to help evacuate their kids.
In contrast, a regular state-mandated K-12 education puts a classroom full of kids under the sole lie-safety responsibility of one adult teacher. With that in mind, the life-safety issues of an "E" school use are different than an "A3" Sunday School occupancy.
None of this is stated in the code - - it's just anecdotes I've heard over the years as to how the code came about.
Plus if you call a real church an E now a days,,,, The cost would go way up and you might have a funny looking building