The characters and concepts in Wicked, just like the characters and concepts in our lives, are complex not singular. The implications presented in Wicked provide thoughtful debate and are not meant to necessarily be defined. I find the fact that Maguire has written Wicked in a style that allows us to make our own interpretations stimulating and challenging. But when something is too open to interpretation, it somehow becomes less challenging for me. In Maguire's case, he's talking about anything we want him to be talking about.
Persecution is bad, check.
Power corrupts, check. You shouldn't judge a book by its cover, check. Crimes committed by the religious are often worse than those committed by unbelievers, check. So far I'm missing the concrete, specific allegory and only seeing generalities. That may be due to poor reading on my part, though.