Hugh Jackman's character would have been killed in real life
Travolta had no way of knowing that Jackman would get the lightning quick thought to go grab the RPG and shoot down the chopper.
In reality, Travolta's man would have just shot Jackman right there in the chest after Travolta said "things don't always end the way you think they should."
Boom. He's dead on the roof. The end.
Jackman has too much info in his end and is a giant loose end that a crazy guy like Travolta would not just let be alive, no matter how much he "likes" him.