I was thinking along the lines of using a large mosfet to limit the current (via suitable control circuitry) to (say) 3A and then fuse it as the original poster suggested.
The limited current would still provide ample to blow the fuse, but *may* limit surges so that the controller is not damaged.
Seems like a fairly complex solution though -- although, depending on the cost of the motors and controllers -- it may have a fairly short payback period.
If the short is transient though, you may find that the fuse keeps blowing (regularly, not immediately) and the motor seems perfectly OK.