Made even worse if you pay attention later in the film, where you briefly see that Maya's desktop picture is her and Jessica hugging.
Ammar, a tortured islamic prisoner almost deprived of food and water, squeezing a simple orange juice bottle as it is the most precious treasure in the world and wishing that the torture stops at once. In fact, all the scenes involving his torture are a mix of this and Nightmare Fuel. You just feel bad for him even if he had anything to do in terrorist attacks.
The ending with Maya quietly weeping aboard the plane. She spent years hunting Bin Laden to the point where her entire life revolved around it, along with losing a close friend and being willing to authorize torture in the process. With Bin Laden dead, Maya now has to face the prospect of living beyond it. Add in the fact that no one else is aboard the plane for her to even celebrate her accomplishment, and its not hard to see why Maya is crying by the end.