It was a political move, she would have become the next Jarl regaurdless of if the Empire had supported her or not. It was just best to try to get on the good side of the future Jarl, but the same can be said about Thongvor and the Stormcloaks who is equally unlikeable. Being openly opposed to someone who you hope will fight for your cause is not a good idea. I doubt either Ulfric or Tullius embraced either of those choices.