Her smile tells me she did poison him before returning to the past, because she gains nothing by poisoning him now. Unless he becomes a liability.
Given the book she had Bill copy, it look like it has something to do with the magic she used to go back. Is it a precaution?
If the Emperor did all that, he is a dirty rat. He killed his own children? That's some low down shit. Given how scared the mother was of the Empress, she isn't someone to mess with. I hope she lives up to it and is an ally, so we can watch two boss bitches do the damn thing.