This is a very difficult matter from many different perspectives, not the least of which is the dilemma of bucking a system that appears to condone behavior that is inappropriate at best, and very possibly illegal or unconstitutional at worst.
 
I strongly recommend educating yourself further by reading the articles suggested in Ms. Graab's reply.  Once you are fortified with more information, you will need to decide whether you want to deal with the conflict and notoriety you might vibe up by exerting pressure on the officials in your district.  Your willingness to engage in controversy or experience negative blow-back (maybe even outright discrimination) is important to consider. Depending on how much you want to push, how much time and money you want to spend, you might find it helpful to contact a lawyer.
 
I would also suggest talking to a clergy person of your faith to review aspects of this problem and receive emotional/spiritual, as well as practical support around dealing with the issues embedded in this type of situation. In addition holding conversations with your son, your family, and trusted friends may help to yield ideas and strategies that you may not yet have considered.
 
The tough reality is that historically children of all races, creeds, religions, and beliefs have experienced unfair and discriminatory practices to varying degrees in a variety of social,political and cultural circumstances. While these situations can make a conscious, conscientious, and caring parent furious, the outcome for the child does not have to be negative.  
 
You have a bright and accomplished son.  He is on his way to life success.  Perhaps this experience can help him learn about history and human nature in a way that will empower rather than impede him. The discussions you have  about: 1. how to handle this class; 2. how to handle himself when others try to impose a belief system; and 3. how to hold on to his sense of himself in a situation where he is in the minority, can benefit him throughout his life. Good luck with this.  I would like very much to know how this goes for your son and for your family.
 
Bette J. Freedson, LICSW, LCSW, CGP