Well, being teleported away does underline that the stones interact with Roderick and Scarlett in a special way, so it's not completely bad. However, as you say as well, it interupts the flow of things a bit. So maybe a better solution would be to keep the lightning (and some comments about it by our chars) but instead of teleporting them away directly, either make ZixZax appear a bit later to look for what just happened there(after we have finished whatever we were doing) or make ZixZax teleport them away later?
And yes, it would be better if NPCs noticed that you just vanished into thin air.