So Im not sure if this still is the case, but in the past if I remember correctly, when a faction ship is destroyed it would conventionally be put back to its origin, and then the owning organization would have to repurchase it. Im not sure if theres a method, but I'd like if either designation had to be changed on the ship (essentially meaning no more static name on the ship) or the ship had to be "recommissioned" via immortals. Just to make space combat a little riskier for everyone involved. Basically, you can lose the ship and it goes to a landing pad for immy to hold until someone with bank power can purchase a "new one".
TLDR: Make ships that are destroyed in faction war go to an immy only room, and change name of ship to simulate destroying the ship