Trevalon,
I wish you and Ed the best. (By the way, e-mail me for more things to pull on each other.) I think there have been several valuable suggestions. Follow up on the links and gather your materials.
Also, I think organizing parents and calling in the ACLU might work. However, you need to be fully armed with statistics. While my high school did have a gaming club, we did have to deal with misinformation. In life, the truth is one of your most valuable weapons.
Based on what I have read and heard, it seems that your assistant principal is on a power trip, using her faith to justify enforcing her opinions on others. This is sad, but the same actions have been taken by people following any number of theistic or atheistic belief systems. In the case of the assistant principal, I believe she may be having a love affair with power. That and she seems to make the Borg from Star Trek seem subtle. (Okay, she is slightly more tolerant though perhaps as predictable.)
My advice is to initially use the public library system. My friend Jim (whom I should try to get to the boards, but that's another story) and I ran several games at Chicago Public Libraries in the early 1980s. One thing we did was ask players to check out books, which increased circulation. (This looked very good for the local branch library with the higher ups.)
You may have an ally in the principal. Gather your facts and talk to him. It seems the AP may be violating your legal rights. If you do not fight for your rights, you may lose them.
As for the religious debate here, I will remind people that this is not Nutkinland. (If you want to debate religion, carry it over there.) I will say that as a practicing Reform Jew, I find some of the religious arguments used against RPGs to be utterly puzzling. I mean this is a game where players succeed by mutual cooperation using characters with diverse skills. This resembles many real world endeavors. Indeed, I find the people who focus on the evils of role playing to be absurd in a world with real evils that need to be combatted in many ways. (Perhaps your assistant principal has not heard of news reports. Or of hunger, poverty, disease, or bigotry.)
Jason, I don't know how I can help, but you have my help if you need it. I would like to ask all educators and clergy on these boards to give Jason advice. (Or if you know anyone who is a gamer and is either in the clergy or an educator, ask for there advice.)
Sorry if this went a little long. Good luck and please keep us informed.