I've chatted with agents at conferences and found that most who work with fantasy, fantasy romance, erotic romance and similar genres have no problem working with Pagan clients. Many will mention an author or two that they already represent who is Pagan or Wiccan. I think what you may be seeing is that regardless of their feelings about Paganism, they will still choose to represent authors and books based on what sells in the market. If a fiction work with a Pagan theme can appeal to a wider market, the chances of selling it increases greatly because the number of buyers has increased.
An agent's job isn't really to understand magical workings but to know if any of the big markets out there are currently interested in publishing books featuring it as a topic. If the publisher's interest isn't there, they can't sell the book. It doesn't just happen with Pagan topics. I've had agents tell me they weren't interested in seeing my mystery novels because those aren't selling and ask if I have romance or can make the mysteries into romantic suspense because those sell better.
A similar thing happens with Pagan non-fiction. If the largest publisher is Llewellyn and there isn't much competition in the market as far as advances offered for books, agents aren't going to be interested. Because they just aren't going to make money from representing the book. Understanding magical workings won't change that.