Here's my best (long winded) stab at an explanation:
The canon does not necessarily have anything to do with shipping. If there were no shipping communities than the canon would still exist. The canon is the story as written by the author. So in the case of the HP books when anyone is talking about the canon, they are talking about the story and the characters and the literary choices as they were written/made by the original author Joanne Rowling.
So hypothetically speaking: If JKR had chosen to write a relationship between Draco and Dobby then that would have been part of the canon. OR If Voldemort had lived and killed everyone else off when Rowling wrote the books, then that would be considered the canon. If padfoot had instead been named puddlefoot, then that would be the canon.
Essentially the canon is what she wrote... it's her books in her words. Couples are PART of the canon, but they don't have to be. If she wrote the stories without having any of the characters become couples then the story she wrote would still be considered the canon. Someone who remains "faithful to the canon" remains faithful to the choices that Ms. Rowling made when writing the books.
Shipping is something of a fandom creation when fans support relation(ships). The word ship is derived from the word relationship. If someone "ships" the "canon" then they support the relationships that Jo Rowling made. Therefore they would "ship" Ron and Hermione and Tonks and Lupin and Harry and Ginny. Those would be examples of shipping the canon. A person could also ship Ron and Harry and still be true to the canon. IF they support Ron and Harry's friendship they are still shipping the canon. If they wanted Ron and Harry to marry eachother than they would not be shipping the canon. So shipping is just support of a relationship.
If someone read the books and wanted Harry to end up with Hermione or Dumbledore to end up with Ariebella Figg, then they might "ship" those couples. Acting as proponents of those relationships by voicing their support in a shipping community like this one. Those ships would be in opposition to what was written.
I myself ship the canon. I support all the choices that JKR made in her book. That doesn't mean it has anything to do with continuing the story from the books though. I don't write fan fictions. When I discuss the books I just support her choice to put Ron and Hermione together in a romantic relationship and her choice to put Harry and Ginny together in a romantic relationship.
I hope that helped and wasn't too confusing Thessalie. I'm sure it could be explained much better by someone like Dumbledore's Woman (Katharine) or Galadriel (Sabine).