Ahh... I see now.
yeah, that's a toughie...
I recently had a mission where the player had to run around an area marking a minefield. I put the waypoint right in the centre of the area, and made sure it was out in the open.
I figured if I made it as clear as I could that the waypoint wasn't supposed to mark the position of any mines, the player would realise they have to do a bit of legwork. I just had the waypoint as a hold waypoint, displaying the test "Mine field".
I'm not sure it's possibly to turn a waypoint 'off' in cadetmode... short of getting the player to join a group that doesn't have any waypoints (you could make the player join a group by themself, and then join them back afterwards).