Not siding with the school, but there are often regulations through the health department about outside food in school kitchens. As a former SPED teacher, we had a separate fridge and microwave in my office that my students brought from home. Think of it this way: if another child's soup had been warmed up in the microwave prior to your daughters, then cross contamination would be something that would upset you if it happened. As long as the school follows through and no outside food is allowed in the kitchen by ANYONE, then there is no issue of discrimination or unfairness. However, since celiac is covered by the Americans with Disabilities Act, the school should provide reasonable accomadations for her regarding eating. ( but the accomodation cannot override health department or state.regsmregarding the cafeteria). I know in some states, the school has to provide your daughter a gf lunch. If thats the case, then as a parent yoou have to decide how comfortable you are that her lunch is being prepared in such a way as to avoid cross contamination.
You can make the school make sure her environment is safe at lunch by having the school specially clean where she will be eating. That means with a nontoxic, gf cleaner using papertowels (not rags or cafeteria clothes/sponges that ma be contaminated). That would mean where she sits, tabletop and seat, and around 3-4 areas around her bc of contamination. Also, they would need to sweep under where she will sit. These are things the school would havento do as accomodations for your daughter. And if they try and give her "special seating" to get out of the cleaning, that won't suffice. First off, they would still have to clean. And under ADA, she cannot be removex from her peers if reasonable accomodations can be made for her to stay with her peers. And since they have to do the cleaning no matter where she sits, then she gets to still sit with her peers.
Don't know if that helps you out, or makes you blow another gasket. Either way, good luck!