he didn't actually get into the chopper. That dead body in the freezer that looked like Travolta's character you saw earlier was set up to make his death look like just that. They actually escaped down a stairwell when everyone was looking at the chopper.
It was all planned out. Travolta was taking the chance that someone would take down the chopper and presume his death. Then, because no one was looking for him, he was able to start his anti-terrorist raid on the world.
Travolta and his men escaped. DingleBerry escaped with him (and wasn't CIA after all)
Get it?