No way to do that out of the box, but if the waypoints are being used by a script that uses the waypoint data, then you can code any logic you like as the waypoint data can be intercepted. The only wrinkle is that the waypoints do not have any names, so you will not know which waypoint is which, except by virtue of where they start and their nodes are located. You 'could' encompass the waypoint in marker zone, which 'does' have a name, and use one to identify the other, and then do any logic you like with the waypoint data, but you can imagine all this requires some serious ninja LUA scripting skills. Perhaps you can add a feature request on GitHub which suggests how you would like the path system to be improved, which I imagine would include giving waypoints names so that they can be activated/deactivated through the IFUSED field meaning you would not need to do any coding.
GameGuru Classic will continue to be supported with bug fixes and functionality additions.