So which slave is it that you need to kill?
Reading the various threads related to the Iksar Shaman Skull Quest #6 yielded very few clues.
When I arrived at the Goblin cave (the deepest one to the right from the entrance), the following two slaves were up (when facing into the cave from the tunnel entrance):
On the left: an enslaved iksar.
On the right: an iksar slave.
I killed the an iksar slave on the right first. Then after clearing the cave again, I killed the an enslaved iksar on the left, which took a while, because he has high resists (resisted my DoTs and half my DDs). Just before he died, a crazed iksar slave spawned on the right and aggroed, so I had to kill him. Neither of these slaves dropped the skull.
After clearing the cave again, an iksar slave spawned on the left and a crazed iksar slave respawned on the right. I pulled and killed the an iksar slave on the left side (again, as viewed when facing into the cave from the tunnel). This an iksar slave dropped the skull.
Conclusion drawn from limited evidence:
Left spawn alternates between "an enslaved iksar" who is needed for a crusader quest and "an iksar slave" who is needed for the shaman quest. Both of these give negative iksar faction when killed.
Right spawn alternates between a different "an iksar slave" and "a crazed iksar slave". Only the crazed iksar slave gives negative iksar faction when killed.