My money is on Kellhus himself. He pretty much ripped apart portions of Sakarpus without breaking a sweat, so Ishual probably wouldn't have been able to withstand the meta-gnostic H-bomb he could unleash. The deeper question for me is why? The most obvious reasons have already been stated, but what about this?
The level of in-breeding that must have taken place in Ishual (a closed system) for 2,000 years would pretty much ensure that everyone's blood was mixed together. I highly doubt there would be any 'pure' bloodlines there. How could there be? And why would the dunyain care to maintain separate ones? So my postulation is that all dunyain in Ishual were, more or less, Anasurimbors. Why else would the dunyain send Moenghus out on an errand, find that he's been corrupted, then exile him. He obviously wasn't that important to the society. Then, years later, he demands his son be sent to him. Again, the dunyain send another Anasurimbor away. Anasurimbors must have been ten-a-penny in Ishual.

So, Kellhus, not needing the headache that would come from a village of Anasurimbors 'returning at the end of the world' prompted him to wipe them all out.
Anyway, that's my crackpot theory.