There are many ways you could do this. I would do it using a switch trigger and a random number.
In your init.sqf file or in the init field of any unit, type:
route = ceil (random 2)
Then create waypoints for the first route, making sure that the last waypoint for that route is of the type "HOLD." Next create waypoints for the second route, ignoring the fact that it looks like these waypoints are ordered after the unit has already taken the first route; if the unit takes the first route, it will stop at the HOLD waypoint, never reaching the waypoints for the second route.
Now create a trigger of type "Switch", the condition of which is the following:
route == 2
Now simply synchronize this trigger (F5 mode) with the HOLD waypoint and you're done. 50% of the time, the unit will take route one, the other 50% of the time it will take route two.