The faction founder may be able to end a war with an NPC faction by accepting war reparations. To see if a request is open to do this head to the command window and open the requests section. Any requests for war reparations will be listed.
The terms of the war reparations are related to how angry the NPC faction is with yours and it proportional to what your faction owns. The terms could include treasury credits, research points or entire systems.
Once accept the war will immediately end and all combat will stop. The agreed war reparations are taken immediately as well.