We, the player, may know it’s pretty cut and dry. The characters did not though.
This is the 3rd to the last quest in the zone, where the Alliance openly admit to not having a clue what Sylvanas wants.
The very next quest:
the Alliance figure it out. And the final quest:
Is the confrontation.
The attack on the Horde flagship was solely for revenge. Justified revenge on Genn’s part, but lets not kid ourselves into thinking that it was all fine because it turns out Sylvanas was doing bad things.
What happens if Blizzard writes that Teldrassil and the elves in it were a Old God instrument and all the elves in it were slowly infecting Azeroth so Sylvanas had to put them down? It would feel pretty dirty for people to say “Oh well ya she burned the tree and it was terrible, but LOOK! she was totally right in the end so it’s all fine!”.
Being retroactively justified is a very slippery slope.