I have no problem with you disliking it (opinions and all that), but your opinion seems grounded in faulty reasoning. Just because it's a fictional world doesn't mean that you can just reject logic and the reasonable progression of characters and their dynamics as the world changes around them.
Well i do not reject logic, i just reject "real world" logic on a fictional setting. Nanoha and Fate being enemies just seems very wrong for this setting. Just looking at that makes it feel wrong to me. That is not the Nanoha franchise, it is a fanfic. Of course, anybody can write one and everybody is free to enjoy it (or hate it).
I just can't see that characters going that way. That development does not convince me that both would go this extreme way. Neither would Hayate. They would find a way to work together. Sure, they would disagree on certain things but never actual fight. It is a forced plot to make an edgy and dark Doujin for the sake of being edgy and dark.