A falling out with Minfilia over Ishgard specifically, maybe not so much.

However, if what I personally have suspected for a while is true IS true, then with this series of patches, likely Part 1 on Tuesday even, we are going to get a much fuller picture of what Mothercrystal Hydaelyn "is" and why the Ascians seem so bent on specifically removing her/it. Remember, they don't want to "destroy" the world; they want to restore it to its "original state", one that evidently lacks the Mothercrystal entirely. And there's been some hints that Hydaelyn hasn't been telling us everything and has been keeping it deliberately simple.

It's very possible whatever we learn could lead to a bit of a split in opinion in how to proceed. Though personally I don't think it'll happen just from a meta perspective; the game's spent too much time building the Scions as characters to just toss them aside.