I don't have any advice for the school, but one of my internet friends has a slightly-older elementary-aged kid with migraines. At the advice of their doctor, they've been supplementing with:
- Vitamin D3: 1000 IU/day.
- Fish oil: 2-4 grams/day.
- Vitamin B2 (riboflavin): 200mg/day
- magnesium: 500mg/day

It's apparently worked really well. Before that, they'd gone through a slew of medications, with mixed success.