The Divine Bell incident precipitated Dalaran formally joining the Alliance. And lo and behold, the Silver Covenant was able to act openly against the Horde.
Legion saw Dalaran returning to neutrality however. And the Silver Covenant did not participate in the battles of that war. It’s almost as if the Silver Covenant must abide by the position of the ruling body of the city they live in.
As for the mages protecting the battleship or the portal master, those were non combat roles weren’t they? And they weren’t Silver Covenant either, they look like part of the extremely few explicitly Alliance loyal high elves who in total mustered four npcs throughout the fourth war, only two of whom had names and only one of which actually fought.