Well, we are Scientologists so I really do understand what you are going through. Our beliefs are different than the Christian ones, and on top of it the tabloids and internet spread around false data about us.
We have taught my stepdaughter tolerance by teaching her about the Christian religion as it is different from ours. For example, we say "Some Christians believe that you go to heaven or hell when you die, and we believe that you are born into a different body. Both beliefs are okay." By letting her know what others believe, and that it's okay for them to believe that, we are teaching her tolerance. And we are not letting her be ignorant of other religions. Ignorance breeds intolerance.
It's interesting that she'll get into conversations with other kids about religion and her accepting attitude is contagious.
We are also teaching her as much as we can about our own religion. So when some kid says "oh, that's the religion where you believe in aliens!" then she can intelligently say "that's not true. In fact, we believe..."
From having to defend my religion to adults, I have learned that simple truth can turn someone who is ignorant and intolerant into someone that has the true facts and can see how they were believing false data.
So, in teaching your children about your religions you keep them from being ignorant if questioned or made fun of. By teaching them about other religions you can teach them tolerance. And when they can SEE that someone is just ignorant, they will not be jaded. In fact, they will probably just pity that person.
If I were you, I'd send some info about paganism to the teacher. Perhaps she's not as smart as she thinks???
Good luck!