I think it is going to be an interesting transition as Alaska Air decides how to absorb Virgin America. In fact, it is looking like a strong possibility that Alaska might keep Virgin America separate. That approach would not be unheard of. This model is partly what they have done with Horizon (but Horizon is really for the most part an absorbed brand from a customer experience as you book Horizon flights through Alaska).
Below is a very Un-Alaska like video that Alaska put out to start the conversation with Virgin America customers.