It is amusing. It is exactly the thought I had when learning the hero Westley was the Dread Pirate Roberts (though it was obvious to us a lot sooner).
Basically the comic is taking a sane approach to a sweet innocent young lady learning that the “noble guy” is a pirate, i.e. a villain. You know, a murderous bastard who hijacks ships at sea, plunders them for loot, and often kills or rapes or such the crew and passengers. The part about “for the sake of the narrative” is just playing on how to justify the turn of events, and xkcd breaking the fourth wall - something they do a lot.
