@Darkmeep : Did you forgot how the church is on the empress's side? During the trial? Or that the person who brought Eli out was that priest guy?
The empress clearly said it in such a way that even if they correctly guessed her intention, she can say they're just being paranoid since what is written is vague enough to be interpreted in other ways.
Even if the emperor know, he can't recklessly act against the church. I'd say look at history, but even at present days you can see the influence of 'religion' on people.