ramme,
It is absolutely true that the Captain does not have to accept anything he or she considers unsafe, e.g. the fuel load specified on the Computerised Flight Plan. I would think, however (in the absence of any other mitigating information), that the Captain would have little justification to put forward to the Chief Pilot in a tea and bikkies session subsequent to the occasion that you describe.
Few of us find it desirable to fly with a well aft C of G, but, as I see it, if the aircraft was within it's Weight and Balance limits, however undesirable they may be, and there is little justification for the stand taken by him / her. There is a quite reasonable buffer forward and aft of the specified C of G limits, and a flight right at the Fwd or Aft limit should be perfectly manageable with a comfortable safety margin.
"Desirable" is a comfort factor, not a safety factor.
Old Smokey