The plumber should connect a section of cast iron flue pipe (available from stanley) to the back of the stove and connect a 90degree bend to this flue pipe and face this up the chimney shaft. At this point the bend should be sealed up against the sidewalls of the cimney shaft. This will stop any debris that may fall down the chimney and into a void underneath.
Heat resistant mastic can be used to seal the joints on the pipe and the pipe-stove connection. The opening in the fireplace can then be built up with fire resistant/concrete/brick and plastered.
The bend on the pipe will give you access to the chimney for neccessary maintenance, cleaning etc.
Hope this helps. Hard to visualise the job at hand.. This what I would do if I was installing a free standing stove.