You don't put stars in supporting roles unless the lead roles shine bright enough not to be outdone.
In Indy 4, Harrison Ford's long-awaited comeback as an iconic screen hero was more compelling than a fantastic actress playing pantomime. So she was fine as a supporting actress.
But in a sequel to the Dark Knight, the compelling faces will be the ones we haven't seen before - the 'who've they got for this one?' faces. It's a curse of sequels that the returning characters aren't the ones people are looking out for. If you have Cate Blanchet as a support to a supporting role, you're distracting from the supporting role, and distracting from the lead role. Her star status would increase this massively. Sarah Essen would have to be a bigger character if Blanchett was involved because she'd attract too much attention to herself.
Example, the Chechen. Great character. Really nailed his performance, could easily have been the central antagonist of another movie - but no-one came out of the theatre thinking, 'I wonder why they didnt develop the Chechen?'. People were remembering how the Joker dealt with him, or how the Joker compared to him. short, he fulfilled his role of supporting a supporting character (The Joker).
Now imagine that he was played by Robert De Niro. The Chechen's performance had many Robert De-Niro-esque mannerisms, so it's fair to say that Robert De Niro would suit the role. But De-Niro in exactly the same role would ruin the character - not because he couldn't get the performance right (I think the fact that he could is unequivocal) - but because everyone would be thinking; "what's gonna happen with De-Niro", and feel dissapointed walking out of the film because they didn't get to see enough of him.
In the same way, Cate Blanchett in a role that is supporting a supporting character would be equally as distracting. Sarah Essen (were she included) would be meant to support the portrayal of Gordon - she's there to develop him as a character, not to shine as a brilliantly conceived character on her own.