I have a feeling this isn't what is behind the father's lawsuit. It's probably more like "suppose his daughter is assigned to sit next to a nerd or an uncool student". Likely religion or race have nothing to do with it --- she's at school to be cool and wants to hang with the cool kids. Likely the school has had problems with the lunch hour and kids forgetting completely what school is supposed to be about.
Do the teachers have assigned seating for lunch as well, or are they allowed to freely associate with whomever they want? One of the arguments against home schooling is that the kids miss the opportunities to develop social skills. Forced association is worse in my mind than no association. How much confidence and comfort will the children have in their lunch neighbors that they will open up and enjoy the experience? How much of their total lunch period are they subjected to the forced association? If assigned seating is okay for lunches, what about on a school bus? I could make a better argument for assigned seating on a school bus for safety reasons than the needless oppression at lunch.
I get the feeling that the faculty at this school has assigned seating for faculty convenience. They do not care if they alienate the students. And alienated students are not the most receptive to classroom instruction. To the faculty the kids are just an inconvenience they have to put up with while they pass the time necessary to earn their salaries.