Let's start by defining what subverting expectations actually is.
While reading a story, people form certain opinions about the characters and speculate about what they might or might not do in the future. Those are expectations.
Expectations are subverted when the actual outcome differs from the expected outcome.
People value different outcomes according to their own internal criteria. Some people don't like it when their expectations are subverted because they enjoy predicting the plot correctly. Some people like it when their expectations are subverted, provided that the actual outcome, when evaluated against their internal criteria, is superior compared to the expected outcome.
It's hard to objectively assess outcomes but practice shows that there is some overlap between how different people assess them. Case in point, most people agree that the Last Jedi and Season 8 of Game of Thrones sucked.
Now, subverting expectations is good when the actual outcome is better than what people expected. When the actual outcome is worse, it would have been best not to subvert expectations. Let's take a look at a few examples:
1. The Burning of Teldrassil
Due to the intentional ambiguity surrounding the Burning of Teldrassil that was created by Blizzard themselves, people expected it to either be a false flag by the Alliance or N'Zoth's forces. Turned out that there was no twist at all and it was just Sylvanas going crazy. Were expectations subverted? Yep. Did people like it? No, it fucking sucked.
2. The Siege of Lordaeron
When Sylvanas started to blight bomb the Alliance, people expected Anduin to pull a deus ex machina out of his ass to save the day because the outcome of the Siege of Lordaeron was already known. Just like people expected, Jaina showed up and deus ex machinaed the Alliance not once but twice. Were expectations subverted? Nope. Did people like it? It was meh, bad but not as horrible as the Burning of Teldrassil. Could've it been great? YES! Just have Anduin bring gas masks and show that he is a competent military commander (therefore subverting people's expectations of him being a moron that has to be saved by aunt Jaina). But nope, Blizzard sacrificed potential character development for a "cool, badass moment".
As we can see, sometimes expectations have to be subverted but other times it's best to just give the fans what they want. Too bad Blizzard writing team is holed up in their sacred, negativity-free "dojos" and won't hear any feedback. A shame really since in the past they did show that they are capable of delivering a good twist. Case in point: Illidan tearing a rift to Argus was not wholly expected, was foreshadowed beforehand and totally fit Illidan's MO.
tl;dr write a story that the FANS enjoy, not literary self-wankery.
bonus point: civil war stories suck in general because they are character-driven stories and therefore lay bare everyone's motivations. When your characters are one-dimensional cardboard cutouts, civil war stories devolve into complete shambles like BfA where it's one "MUH HONOR" dumbass side vs. another "MUH GENOCIDE" dumbass side.