This is unfortunate all the way around. Nobody walks away from this one without some injury, some stain upon their reputations. The following, while not entirely judicially prudent, nor perfect, is the most likely result, barring any new developments or evidence of substance:
With names and events out in the open now, the airline is forced to act responsibly. Most likely Pena will receive an out of court injury settlement, the captain will either be fired or forced to resign, possibly with his retirement intact, and the airline will be vilified for using poor judgment, having more apparent interest in their own image, than the protection of their employees.