Yeah, kind of convoluted. And who is the antagonist, the master mind, the alpha terrorist of the whole collective terrorist conspiracy?
You've seemed to have trapped the pilot squarely between the horns of an authentic dilemma, between two 2 sets of stakeholders in the outcome of the his choices, the family and the passengers, between 2 equally undesirable outcomes. Dilemma in drama is always a good thing, and it's the aspect of the story that most intrigues me.
You mentioned 2 options: save the passengers (and himself) or save his family (and himself). What about a third option: he saves both the passengers and family -- by sacrificing himself? He wants to save both groups of stakeholders and himself (objective goal) -- but he finally realizes that he can only save 2 out of 3. He must rise above his character flaw (subjective need) and sacrifice himself for the others.