Just to be fair I will take the other side of this because I know a family dealing with the same issue. This child was in a daycare centre since age 1 so used to a group, separating from parent etc without issues. His JK class has 40 kids in it and a teacher and EA so he went from a 1-12 ratio to a 1 - 20 so that is part of the problem but the most is the noise and confusion in the classroom is just too overwhelming. The parent has had the chance to visit the school and observe from outside and seen days when child was fine sitting in circle/storytime or painting etc but other days when kids were more restless in unorganized free for all "freeplay" and he was cowering in the corner unnoticed for the most part.
Can you get her talking about school and the parts she likes and the people she likes and the parts that are her least favourite and see if you find some patterns.
I agree that the option to just stay home is not helping in that she doesn't have to face her fears.