The writing in a lot of the novels, especially with Jaina and even Sylvanas, should be taken with a grain of salt, because their impact in the actual game story has always been haphazard at best.
Jaina’s threat didn’t make much sense because Dalaran had already taken the side of the Alliance against Garrosh by the time War Crimes was written, but had only pledged them because Dalaran’s neutrality had already been violated in the course of the war, and the Horde under Garrosh showed no qualms using powerful and destructive magical artifacts to win, which is kind of Dalaran’s whole reason for existing (making sure people don’t do that).
It was a natural thing for Dalaran to go back to being neutral, or at the very least apart from the Alliance as a whole but still favouring them over the Horde. A comparable example would be the goblin cartels, who, while neutral, only have their zeppelins available to the Horde itself, as opposed to both.
Dalaran, given its role in modern day Azeroth (at the time, anyway), benefits far more from being detached from any one faction, as opposed to within the Alliance structure, since they could very well one day need to bring the Alliance to heel for using dangerous magical artifacts irresponsibly. And they did go back to being relatively neutral by WoD, since Horde players can go into the Kirin Tor outpost in Talador, albeit only after Jaina grinds her teeth about it.