Achilles was a mighty warrior, but his Achilles' heel was his heel.
In Christianity, Apostolic Canons were ancient laws and decrees, usually enacted by consensus of bishops and Ecumenical Councils. The most well-known decrees have led to definitions of Biblical canon, [Gk: κανον] traditionally referring to the books of the Bible (Old Testament and New Testament) which are generally accepted as being doctrinally sound, worthy of inclusion by church bodies, and proclaimed liturgically. Non-canonical works are known as apocrypha or "Deuterocanonical" (works which, while perhaps edifying and ancient, are doctrinally rejected by some or all Christian authorities). The writers of the New Testament and other Church Fathers had adopted the Greek word for a type of straight reed, κανε, because it was being cut and used in the Hellenistic world to apply standards of measurement.
The term "canon" was subsequently applied by analogy to the Sherlock Holmes stories which were written by Arthur Conan Doyle, as opposed to the adaptations into other formats (stage plays, films, etc.) and non-Doyle stories. An early example of this connection was in a 1910 satirical essay by the Catholic scholar Ronald A. Knox, Studies in the Literature of Sherlock Holmes.
From there, it took on its modern, even broader meaning for fiction in general: the material widely accepted as created by the recognized author(s). For instance, Star Wars canon comprises the films and some TV shows made by Lucasfilm (and Disney after its buyout of Lucasfilm), but that canon is supplemented by a large amount of non-canonical Star Wars content in other media such as books, video games, comic books, fan fiction, etc. In addition, what is canon can be changed, as occurred when a large portion of formerly canon Star Wars content was decanonised in 2014 to make narrative space for the upcoming Star Wars trilogy sequel movies. Determining what is canon and what is not in a narrative framework has a tendency to excite huge passions amongst fans where they decide what is, and what is not, binding to the fandom, drawing comparison to the huge factionalism of religions.
Here, Cueball is using the modern meaning to describe a theological dispute from the 18th century when scholars used canon in its secondary derived meaning referring to the canon of Scripture. There are many examples of fierce theological disputes that were recorded in pamphlets and books throughout the 16th to 19th century, for example just regarding the correct mode of baptism: 1644 (683 pages), 1646 (342 pages), 1697 (150 pages), 1768 (219 pages), 1831 (400 pages), 1874 (107 pages) - examples selected from hundreds of similar books. Similarly, the word "fandom" comes from the word "fan", which is the shorter form of "fanatic", and '-dom', as in a class of people. Fanatic's etymology, in turn, points to the latin word "fanaticus" meaning 'of a temple, inspired by a god'. (The latin word "fanum" means 'temple'.)
An Achilles’ heel is the weak point of something or someone who is otherwise very strong. It derives from the legend of the great Greek warrior Achilles, who as a baby was dipped into the river Styx by his mother to make him invulnerable everywhere on his body that the water touched. However, during the dipping, his mother held him by the heel, which was thus vulnerable because it didn't enter the river, and in fact Achilles later died after he was shot in that heel with an arrow. The joke again is the self-reference.