I actually completed my Orca kill mission, go figure. What I did was when I first encounter it, I did not shoot and left instead. Afterward, somehow it takes like 20 more USS for the target to reappear in another clean Orca (close to giving up at that point). My rep is quite good so I thought 1 murder should not degrade it much, so before I abandon the mission might as well kill this thing. I killed it (it does not even defend itself) and the mission complete notification appears (along with a bounty on my head for murder).