So, been doing some thinking on the nature of the 4th wall throughout the story. Homestuck started as a story that recognized reader input both in where the plot went, and even by the characters themselves. The characters made references to Hussie's earlier works, and the story recognized the author himself as a character (and a mortal one at that). Now, with how Calliope refers to the kids as "characters", and the fact that she seems to be reading the comic like us, it gets me thinking...
Calli's personality seems to represent fandom in response to a story, specifically to Homestuck. Suppose that Calli and/or her brother become Lord English, and that killing Hussie was a way for her/them to literally alter the plot in an authorial way, as some kind of supercharged 4th-wall-breaking fanfic writer who "assembles followers (ie. fans) to destroy universes (ie. stories) he has marked for predation".
It resonates with Hussie's thoughts regarding user-driven content, and the importance of an author exercising control over it... having the ultimate antagonist of a 4th-wall-breaking story be a fandom which reverse-breaks the fourth wall, and for all their love for it destroys the universe.
So,
Cherubs are inherently aware of the fact that they're in a story... or at least aware in some fashion of the hand of Hussie hovering above them. I think Hussie's Authorial Control over the Cherubs is akin to
the exiles' suggestions and commands to other characters. I guess that's why
LE singled out Hussie in the intermission... he was tired of that authorial bullshit. And now he is a free agent, outside of the control of the author, and free to destroy the story universe which all his hated sister's fanfiction was about (probably because she too had a form of 4th-wall omniscience and was a Homestuck Fan), with the author himself cowering in fear from his own character.
Other Theories: The Cherubs are on
the meteor the kids and trolls rode from session to session on, which they had to abandon in a hurry for some reason or other (hence Rose leaving
her Diary for Callie, etc.) It drifted through Paradox Space and eventually crashed on the Cherub Planet... which is possibly the planet the Humans created/will create when they win their session. And the Cherubs (or perhaps Callie?) creates/has already created the Alpha Troll Planet as an expression of fandom, when their session is eventually won. Thus everything is a giant self-fulfilling loop.