I figured that the bounty would only have applied to the Basalisk soldiers that had gone rouge and escaped Bodes world and there is an advantage to having a beaten enemy alive. Namely being able to point to them and say "These are the last remnants of the most powerful opposing force Hub has ever faced. Do you think you are a bigger threat than them? Do you think you will fare any better?" anytime a colony starts thinking about separating. Psycological warfare is a powerful tool.
Apologies if I got a bit dark here.