[Q]

There is even a easier solution that can be reversed quickly (even within a current game): go to the techarea.txt file and change there for the resupply tech the maximum level from 5 to 4. Then the quantum reactor cannot be researched. The AI will handle this situation without problem.
The increase of the cost would not be too much a problem for the economy with a medium or high AI bonus game, but the construction time would be increased and the AI would not take that into consideration.
The biggest problem for the AI would be a large increase of the quantum reactor size: the quantum reactor usually is one of the first misc abilities in the ship designs and the AI would follow this design instruction even if this would leave no space for other vital components of the ship. You would have to redesign all AI design files and that is a lot of work!!