What everyone's not considering is the incident in Deepholm where the ALLIANCE Was killed by Twilight hammer ad you only find that out because you raise their -ghosts-. And there's twilight hammer swarming the barracks of Stormwind and inside the Cathedral's catacombs AND in the very throne room. Of course we don't know who planned it, or whether it was Deathwing's people or not. It could have been them who started the cannon firing and thus made the other sailors on the ship think it was an attack. The Alliance -never- get a version of the story, despite the rather significant part that they supposedly play in it. If the "Alliance" had succeeded in that mission, Thrall would have been brought to Stormwind (or killed by Deathwing) and before he had a chance to explain the heck was going on.. the world would be broken, the way Deathwing wanted. Honestly, it's Deathwing who has all the motivations to stop Thrall. And it's Deathwing who's proven he wants a PARTICULAR revenge on Stormwind. The title screen even shows him perched on Stormwind's towers. Stormwind was where his daughter was unmasked, where he has the most ties himself. The King of Stormwind, canon wise, is the one who killed Onyxia. Deathwing wants Stormwind to suffer...how better than to infiltrate and let Stormwind's troops look the ones responsible for the very sundering of the world? Remember, only one survivor was left in Deepholm and that was with his insides torn open and you have to tie him to the wheel.

Until it's EXPRESSLY stated by Matthias Shaw or the King of Stormwind that THEY gave the order... I don't buy it. It makes no sense. Varian is a hothead, but he's not the type to go "Kill everyone you see, including possible merchant vessels passing by, and kidnap Thrall, who I magically know is in this location." It just doesn't add up. Sure, if it was GARROSH on the boat, I'd think it made more sense. But Thrall when there's already a warchief in charge? No, the pieces don't fit.