The heli and its crew have all their waypoints, which is good. Get the squad into the chopper, but give all the subsequent squad waypoints to the player, who is presumably going to be the squad leader. At some point in the chopper journey, have something like this in a script or trigger
"[_x] join Player1" foreach units Squad1
syntax almost certainly wrong, but you get the picture. If the player is not the squad leader its even easier, you just make him join the squad.
I'd suggest a bit of titletext or radio chatter to explain the join.
Hope that helps