I think balancing by kills makes sense, more than average damage does in a way. E.g. you can deal a lot of damage, but if you don't get kills, because you allow the enemies to heal up, you don't win the round. Kills win the round. So the person with the most kills does have a large impact. Also changing it to average damage instead would require some rewriting of that system and I'm not planning to do that.
Thanks for the suggestion though.