The Jester was a comically fat and abrasive representative of a part of Jillian Zamussels's subconscious who appeared when she was drugged on Heroine buds. Jack speculates that he was a part of her mind that urged her to action when she was forgetting things.
The Jester might have been Jillian's mental link to Fate and the Titans. Many events in the comic, as well as the utterly bizarre strategy of his side, suggest that Charlie has been dedicating all his resources to opposing them, which may well be the reason he destroyed it.
Jack suggested that the jester was the part of her mind that urged her to action, and its destruction might be the cause behind why Jillian has so much trouble determining what she wants and has arguably become a more simple character in the present era than in the past.