As I recall, the solution to this problem involves building a custom school with multiple School Rabbit Hole doors or rugs. Then they don't clump up and block each other from going through the door.
I don't know a lot about the doors, the rugs were easiest for me to deal with. I believe they need 4 squares all the way around for free access or else they'll still block each other trying to get in and out.
I think a non-mod alternative was to place extra schools around town. They don't take up as much space if you place them in a basement - just make sure the door is inside the basement, the rest of the building can hang out into space though it is better if it is entirely enclosed within the basement. Some buildings have two entrance/exits - make sure both doors are within the basement and accessible.
