I actually believe her actions are justified, when she became the leader of the kirin tor she kept the neutrality. She even refused to side with the alliance when prince anduin came before her to ask to pledge dalaran to the alliance by his father's request.
the time span between the events of tides or war and the landfall of the fleets in pandaria is pretty short, and during this time she (and in extent the kirin tor) has been betrayed twice by the sunreavers. Once during the battle for Theramore and second when they stole the divine bell from Darnassus.
Jaina kept her neutrality while the sunreavers didn't. So she kicked them out of dalaran and decided to side with the Alliance. Her actions are justified, the destruction of theramore was possible with the Focusing Iris. The same artifact that is now kept by the kirin tor. So giving the history of the sunreavers of aiding the horde. The wise decision would be to expel them and ensure that such atrocity can never happen again.
And before anyone says the Baine Bloodhoof said that "there must never be another Theramore" to Garrosh, he would sooner assasinate him like he tried with Vol'jin then actually listen Baine.