The weather simulation in FlightGear is already very simplified and by far in no way realistic.
Just compare it to real weather simulations that are run on super computers like the earth simulator 2.
http://en.wikipedia.org/wiki/Earth_SimulatorBut the simplified weather simulation in FlightGear does do its job.
The same kind of simplification can be used for a simulation of a nuclear bomb explosion.
For example, we already have a way to add wind forces to an aircraft in FlightGear. The same system could be used by a nuclear bomb explosion by changing the wind forces values.
It's only a vector calculation of two forces, the force of the wind and the force of the wind that was initiated by the atomic bomb explosion.
So when the bomb explodes, it will have an effect on the aircraft.
This is feasible to implement in Flightgear.
So i don't see any problems with simplifications like that.
We always had simplifications in FlightGear all computer simulations do have this and we will always have them for ever.
Even a simplified destructible city for eye candy would be feasible, though it is a lot more work than the above mentioned addition to the weather system.
It would require to replace the 3d models in FlightGear in realtime by smaller black painted ones and adding a sort of movement to them. The above mentioned wind vector could be helpful for this.
Referring to the thread question i don't see a problem here in supporting both kinds of simulation, civil and military.
To please the pacifist a trigger would be all that is needed. A trigger that switches the FlightGear simulation mode between military and civil simulation and making the civil one the default active one.