Part 138 does address the issue.
SA CATS 138.04.2 requires the Manual of Procedure to contain specific policies and procedures regarding, inter alia:
'Refuelling with medical personnel and/or patient on board'.
So, the first stop in such a case is the Manual of Procedure.
SA CARS 91.07.13 cannot be overidden unless the SACAA grant an exception and any such exception would be referred to in aforesaid Manual of Procedure.
I would have thought that most Air Ambulances are not using aviation gasoline or wide-cut type fuel. If they are, get a new medivac policy! Accordingly, it shouldn't pose any problem refuelling with a patient on board, or indeed any passengers, just refer to the Manual of Procedure for detail.
Of course, if the refuellers refuse to refuel, without patient disembarkation, there is little one can do apart from using normal diplomacy.