I'd prefer the game just to give us a seleciton popup for the master writs where you can choose which item will be taken.
Adding some protective functions via addons could be possible but you'd need to check so much stuff which could be avoided by the game "from the scratch"! So better build it right instead of having to rely on addons which have to be adapted after each patch again
@Chip
Please have a look at those master writs and try to come up with something that prevents destroying of the higher level equipment due to master writes (even if the item is unbound and a set part -> maybe one crafted a set part for a guild mate, improved it and then suddenly the next writ just will destroy it...).
Maybe a simple "ask dialog" will be enough?