We were this close to being able to make our own judgment calls about what to do from here on. With Urianger taking history lessons from Eldibus, we already had a source of cosmic truth, and somehow I highly doubt Minfilia would have sat around as a useless figurehead during our time in Ishgard. The Eorzean Alliance is kind of her baby. She was also beginning to have doubts after losing Moen, not to mention Eldibus was willing to talk openly with her, so whatever Hydaelyn's motives, she effectively beheaded us for the sake of keeping us on the path we were on. That's... shady.
