He wanted to kill every noble until Vin changed his mind. While, yes, that was mostly as a political thing, he still wanted to do it, and the nobles were regarded as a separate class both ethnically and religiously, checking off the box for genocide. He killed the skaa guards because they were traitors and separate from skaa to him (there is a term for that, I think it was quis-something, from some French guy or something).
Edit: Rusts! @Pathfinder ninja'd me.