Is this the script you're using?
http://www.ofpec.com/editors/resource_view.php?id=316I ask because I don't recall any use of triggers as you describe with this script...it simplifies everything immensely and should be required for all missions involving choppers.
If so, I dunno what to tell you...tried placing some invisible H's? As far as killing trees, you can either take the time to get all the IDs and kill them all in a script - which really doesn't take *that* long - or you can camcreate some nice LGBs over the area to clear it out.
Or, if enemies are nearby, set the choppers to careless, hold fire - enemies tend to spook them into not cooperating.
Choppers are annoying little bastards and things need to be just right for them to cooperate...