I think your forgetting one thing, Bransons interests in Virgin America lies with its use of the Virgin brand in USA. With his name on the tail there is additional licensing from it's ongoing operation.
I don't think Branson's interest really lies in the company itself. its more in the company existing an using his brand where his interest lies.
I think much different words would have left his mouth if Alaska decided to keep the Virgin name after the JV went through.