We see a lot of conflict between religion and magic in this book, which is something that concerned Daniel Defoe, provider of one of our epigraphs. (See "What's Up With the Epigraph.")
A lot of the stuff that goes down in Munchkinland (dabbling in the "pleasure faith," resurrecting old "pagan" beliefs, persecuting people, etc.) resembles what was happening in Europe, and later America, from roughly the 1500s to the 1700s. These were the years of the the Protestant Reformation, when religious frenzy led to wars and persecution (think the Spanish Inquisition and witch hunts). Many of these instances of persecution happened when some über-Protestant/Catholic/whatever went after someone for being a "pagan," or for following older, non-Christian, folk traditions.
This is all something cool to keep in mind when reading Wicked, since it's interesting to compare how religion, magic, and witches are treated in Oz with the way they have traditionally been handled in our own world.
Maguire's depiction of the Emerald City as a place of political oppression, danger, corruption, etc. bears some similarities to postwar Baghdad. (See "Setting" for more on this.) Though Maguire, publishing in 1995, was influenced by the First Gulf War, Wicked the musical premiered in 2003, the year that U.S. military action began in Iraq.
We also learn that the Wizard is Irish, and that "No Irish Need Apply" for jobs in the mystical Other World (5.11.34). What's up with this? Well, in the nineteenth and early twentieth century, the Irish were considered "inferior" and faced a lot of prejudice in both England and America. Irish immigrant communities in America often faced persecution for their Catholicism.
And if you are interested in learning more about the historical context of Baum's original novel, and how it is alluded to in Wicked, check out this online essay by Peter Dreier. The most overt shout-out to this history comes during a discussion of Dorothy's name (5.5.44). Boq notes that Dorothy is a backward version of Theodore, a reference to Theodore (Teddy) Roosevelt, U.S. president from 1901 to 1909. During her recruitment campaign, Madame Morrible also uses one of Teddy Roosevelt's most famous sayings: "Walk softly and carry a big stick." (188.8.131.52). Maybe she heard this from the universe-hopping Wizard.