Yes, it will work. Just create an event that declares when the event takes place, have the dude dissapear. Like this:
1.)Create the two groups
2.)Create an area(make sure you give it a number)
Get the guy to his waypoints by any method you choose
(I'm assuming you know how to get a person to a waypoint)
IF:Group 5 is in area 5
THEN:Redirect group 3 to waypoint list X
Set group 3 velocity to Y
Vaporize group 5
So here's what'll happen.
Once your dude gets to the chopper, he'll be in area 5. The game will then make your bird fly and get rid of the dude.
You could also have him teleport to a far away location so that it looks like he's still alive just not in danger of being killed. Do this if the game decides he's dead.
Hope it works for you. And this should work in both versions of DF