In the 1840's, Philadelphia was kind of a mess. Class warfare had led to rioting in the streets, and things only got worse when two crimes were committed, and the offenders were let off easy, causing many to cry foul, including George Lippard who penned The Quaker City to immortalize the injustice and abomination of the cases. The title is a reference to William Penn, an important quaker in the history of Philadelphia who named the city. The name 'Philadelphia,' is designed to mean "The City of Brotherly Love," and so the title is an ironic accusation against the city for the toleration of such evil. The evil here refers to the forced rape of an innocent teenager, a real crime committed by an important, wealthy citizen who got off with a 'not guilty' by using the infamous insanity plea.
The story is obviously grotesque, involving three separate accounts of vicious behavior, including debauchery, rape, fetishism, and other illicit activities, under the guise of a monastery. This "Monk Hall" metaphor does the same thing as the first title, bringing attention to the ironic reputation Philadelphia had for being a morally upright, loving place. In terms of politics, the work is undeniably critical of the upper class, and most of the patrons of the underground gentlemen's club are wealthy, powerful, esteemed members of society.
Therefore, in a word, the novel is about hypocrisy and the hateful, power-hungry entitlement of the Antebellum upperclass. The novel is intentionally graphic and offensive, because the disturbing aspect is a necessary component of communicating just how unjust and evil the class divide had become in the mid 19th century.