By the time you can launch a planet-killer, you are no longer tied to your own planet anymore. It requires marshaling an amount of energy far beyond what you could afford to do in a biosphere, and a biosphere is all a planet really has to offer. Two of these civilizations might certainly take a swing at each other's planets, but it wouldn't end the war by any means; at this point the planet may not even account for single-digit percentages of what is going on in the system.
I think if you look ahead at feasible technology, you get self-sustaining pure-space civilizations long before you get civilizations that can launch relativistic planet killers.
(The other problem with the "planet killer" hypothesis, as we've discussed in other HN conversations, is that there's no reason to wait until there's a civilization on the other end to launch one, given how fast they can pop up. As soon as you see life, you should launch one. But Earth has been broadcasting fairly conclusive proof that a civilization with just a bit more tech than we have now is alive ever since the Great Oxygen Catastrophe, yet nobody has killed Earth.)