When I first read Edge of Anarchy, I already knew that the queen was the BBG, but I was still under the impression that she was the one who initially recruited the PCs into service. After all, she sends them to Kroft with no obvious reason, so I kind of expected this to develop into a "BBG manipulates PCs, they eventually figure it out, but it's almost too late" situation. Unfortunately, it didn't turn out that way. But I still think it's possible to replace Kroft with Ileosa as patron.
The first part of the AP would go pretty much as written, they would run around doing errands, capture Trinia, get interviewed by Orisini (who sees crown-traitor potential in them)...
In the second part, Queen Ileosa would have the PCs "investigate" the breakout of the disease to appease the public, ghost-chasing most of the time, but eventually they'd pick up the hints that she's behind it. This may lead to a premature confrontation, but Kroft or Blackjack would intervene here, prompting a search for the missing seneschal instead of a suicidal strike at the palace.
From the third part on, everything would go as written, plus the PCs would have the extra motivation of exposing their patron and clearing their names of any association with the tyrant.