After searching the web on pathfinding I stumbled upon a waypoint technique called navigation mesh. If I understand it correctly it is possible to use a* in the same as a waypoint structure but the navigation mesh will give you a lot more freedom for the NPCs. It will also generate faster paths for the characters to walk.
I think it will be quite easy to implement a navigation mesh tool inside the editor so that is what I am going to go for first.
Interested readers can read about navigation meshes vs waypoint structures over at ai-blog.net