Would I be right in assuming it is a "frog" type battery and you can not get the saddle low enough for your wife.
If it is, I suggest the you remove the split plastic lower cover and the seat post clamp and have a sheet metal box formed which can be bolted to the existing 4 fixing screws located on the side of the battery slide plate and then the base of the box could be fabricated to bolt to the rack.
The removed plastic cover could be used as a template to make the metal one.
You would maintain the advantages of the existing system, but rack mounted ie: no wiring modifications, easy battery locking and removal and a secure location for the controller.
If you retain the old parts, it could then be returned to its original condition at a later date, if required.