As seen in this photo (from here) there appears to be a significant scarf to the nozzle.
I'm familiar with scarfing reaction control jet nozzles to fit fuselage contours, but this one is completely external.
It's possible the image of the nozzle is distorted by the camera lens but I don't think so; the aft bulkhead of the fuselage appears perfectly circular.
It is also possible that the nozzle has been vectored up, but I don't think SpaceShipTwo has thrust vectoring, and the exhaust streaks inside the nozzle appear to be aligned with the longitudinal axis of the spacecraft.
