The things they’ve done have been fine mostly, it’s just how those have been written which has inevitably lead into player responses.
Whether it’s old vanilla moments (quiet support for the Scarlets, dwarven imperialism in Alterac/Kalimdor, Theramore’s fake neutrality) or more recent stuff in BfA (mass murder of goblin workers with molten giants, throwing Horde ambassadors into the Void, Purge Squads, murdering goblin socialites at a party. killing a bunch of civvies during the Dazar’alor invasion), the Alliance stuff is generally glossed over by the greater narrative, which leads to players doing the same.
Those moments are just fine as far as villain moments. Just they’re not really treated as such.