A) It wasn't that the sidhe was disagreeing with Harry, it was what he was disagreeing with. Harry told them that they cannot kill or torture mortals -- who are also sentient beings -- while in his presence. The sidhe in question piped up with the equivalent of "you can't tell us what to do!" It wasn't that he wasn't human, it was the fact that he seemed to be active condoning the kidnapping/murder/torture/rape of innocents. Harry would've reacted similarly to mortals who did the same. It would be speciesism if Harry treated the sidhe differently because "ah, he's a faery, that's who they are."

B) The winter sidhe don't seem to respect much aside from violence and power. Harry knew that there was no other way of enforcing his rules in about the two seconds that he had to make a decision.

I really like this.

From a moral perspective killing is "always" wrong, so even the first one was morally questionable.

Depends on whose morals you are using to judge.