I'm glad you described this issue. I just spent five minutes on that map wondering what the heck I was supposed to do next.
I've done some additional testing and have determined that the helicopter "gives up" trying to land if your commando's location on the ground is preventing it. The first time I played through the mission it did this almost immediately, flying off into its own destruction. The second time I was able to recreate this error I was moving the commando explicitly to prevent the helicopter landing. It tried to adjust its landing position three or four times before once again flying off to die.
Just restarting the mission seems to be the best workaround right now. You only have to take out two SAMs to get back to this point.
