It's implied that some members of the Sunreavers are responsible for the bombing of Theramore whereas Dalaran is said to be a neutral city. In Wolfheart, Dalaran even declined an invitation sent by the Alliance to assist to its diplomatic meeting in Darnassus to help bridge the gap between the two factions.
But in MoP, the Sunreavers will try to murder one of the most trusted et talented sorceresses of the Kirin Tor : Jaina Proudmoore... but will succeed in destroying her citiy with all its inhabitants.
The question is : Will Dalaran rejoin the Alliance led by Jaina Proudmoore after the events of Theramore ? After all, Metzen said that Jaina will get a new role in Azeroth.
My opinion about this :
The Focusing Iris (the arcanic bomb that will be used by the Horde to destroy Jaina's tower) was previously owned by Malygos. I think that after Malygos' death, the blue dragonflight decided to give the artefact to Dalaran's magis in order to protect it. In Wolfheart, we learn that after his defeat in Achenvales, Garrosh is ready to destroy the Alliance by any means, by any prices. He could have ordered the Sunreaver to secretly betray the Kirin Tor by stealing the artefact and then trying to accuse the Silver Covenant for having doing this. By this explanation, it's easy to understand why the Horde directly dropped the bomb above Jaina's tower, seeked to eliminate all the lasting survivors, and tried to recover the artefact after the deed was done : no witnesses, no evidences.
"There are Alliance survivors ! Bring reinforcements !"; ... The city is blown up and probably for a very long time ! Why wanting to eliminate everyone, even the wounded ones ? :P
After the loss of Theramore, Jaina will come back to Dalaran, expell the blood elves from the city and take the leadership of the Kirin Tor.