Like I said in my previous post, it wont work with waypoints anyway.
But, in theory you could do as GMG suggested, and make his assumption work.
You can do that by spawning a dummy object, and setting the waypoint to the dummies x,y.
Then if the dummy overlaps the wall, destroy it, and spawn another random position.
You should keep in mind that waypoints add a ton of processing, so if you have many enemies moving around its going to bog down the system.