It will be great!
Another idea is to duplicate the categories functionality if it's possible and make it publishers, so you can add publishers and after that just to select them from a drop down menu.
Yes, the publishers are fletched from amazon, but they will stay the way they are, the categories#2 a.k.a publishers will be just for administration and better filtering.
And other thing, if you guys go ahead and customize these things it will be great to make the internal booklibrary search more specific, with more filters like: search in ISBNs, Authors, Publishers etc.
Thanks for the fast responses, wish you all best and have a lovely holidays!