Both the governments and the clans, especially the elite clans, had to be cleaned up. Elimination might be the best course of action, but that was not what Khal wanted.
Doing so would weaken the overall combat capability of humanity. He only needed the large tumors to be cut off, and the rest could be cured gradually.
In fact, Khal did not see the need to.
Khal and Devion were the most powerful espers, but they could not just use brute force to wipe them all out. They were already seen as monsters, and their intervention might escalate the war even further.
As he said, their involvement only leads to one of the two outcomes. The war ending early or escalating beyond what they could control. There was no in-between.
Ending early brought no benefits. Otherwise, why would they turn a blind eye to both forces' actions?
Khal had been waiting for the perfect opportunity. It was not yet time.
