Question: How can the plane take off from this country airport when they seem so worried about a short landing?
Answer: The plane would not be able to take off from that small airport.
Question: How did the FBI agent know that the two FBI agents on the plane were killed earlier?
Answer: When ground crew, first responders, and police are near the plane, you can see paramedics stacking body bags in an ambulance. It's safe to assume the bodies were dumped after Captain Whitehurst was dumped from the plane.
Answer: It's been a while since I've watched this movie, but he obviously knows the plane is hijacked. It's a pretty safe assumption that the agents are dead as they're escorting a dangerous, high profile prisoner. Pretty easy to connect the dots. Alternatively, they could've failed to check in, and he assumed the worst.
Answer: Planes can take off from smaller airports by power braking. They can hold in order to get within 50% of necessary take-off power.