It seems to me the school has a dress code, not a uniform.
It's important to know the "reason" why the school feels the kilt is inappropriate. Would they have sent the boys home any time of the year? or just during the time of the year when shorts are restricted. If it is because they think the kilt is a female garment, 1, are girls allowed to wear pants? and 2, it's a male garment. Is it because they show your legs, if so, you can make a point for sexual discrimination for both restricting shorts during certain times of the year and not allowing kilts. If it's because they are kilts, make a point for cultural discrimination.