the waypoint will probably still be in effect, unless it's not cycled, in which case, they'll go to the waypoint, and then properly follow the script's instructions. if they're not at the waypoint, they'll try to go to it, but every 10 seconds get an instruction to go to the player's position. if i were you i'd do it like this -
use your waypoints for where they walk, followed by a 'seek and destroy' waypoint, then a cycle waypoint. create a switch trigger activated by the killing of the general. in the 'on activation' field run your script. synchronise the trigger with the last walking waypoint, the one before 'seek and destroy'.
now. your script will change from telling them to move to the player's position, to moving the 'seek and destroy' and 'cycle' waypoints to the player's position, like this -
_huntUnit = _this select 0
#loop
[natashas_group, 5] setwppos getpos player
[natashas_group, 6] setwppos getpos player
~10
?(Alive _huntUnit):goto "loop"
exit
the key is in the numbers contained within the
[natashas_group, 5] setwppos getpos player bit - if your first waypoint is numbered 0, count up to the 'seek and destroy' waypoint, and that's the number. the cycle waypoint will be the next one.
that should work, not guaranteed, and perhaps not optimal, depending on the situation.
edit - the second group can have additional 'seek and destroy' waypoints set too, perhaps around the base, or set along with the first lot, and the same switch trigger can be synchro'd to them. the only drawback is that if you kill the general while the second group is en route, they'll divert course instead of arriving at the destination and
then following.
and aye, mission editing can get like this. fun isn't it