It's a bit tricky to explain but you use the switch property of triggers to skip unnecessary waypoints.
Plot both routes for the unit in sequence - so a north route first then south, (see attached image).
The North trigger is to be synchronized with the first 'Hold' waypoint: Radio Alpha, Once, Switch, named "Go North"
- On Activation: 2 setRadioMsg "Null" <--- in order to hide option South, once North is chosen
The South trigger is to be synchronized with the final waypoint of route North: Radio Bravo, Once, Switch, named "Go South"
- On Activation: 1 setRadioMsg "Null"
In the mission, when North is chosen, the units will make their way there and then stop - because they will not receive Radio Bravo.
When South is chosen, all the northern waypoints will be skipped and they will head south directly.
Advanced
Plot more waypoints after the objective and synchronize an Objective Trigger (Switch) with the final waypoint of route South. Then, after the objective is taken, they will resume a single course whether the southern or northern routes were taken.