We were being hunted by (what we suspect is) an angel. We entered a room with no way back and there were two figures in front of us, shoveling dead bodies into a machine. My character couldn't know that they were normal humans, so I assumed they were some sort of fellow monster (or at least some "things" that were no longer human). Calling the police would have taken too long and my character knew he was too bad at sneaking to get past them unnoticed, so he shot them instead of talking and risking being attacked first.
Of course it turned out that they were normal humans. They were God-Machine cultists who had been murdering people and hiding the bodies in the cellar.
I had a discussion with my fellow player about whether this killing should impact Humanity. Did it count as an Impassioned killing to eliminate those worshipers or not? The motive was to avoid being attacked by these people who were obviously not above killing to keep their secrets, so I felt it was self-defense — Where does premeditated killing of humans end and Impassioned self-defense start?
Does it really make a difference if you don't know its a real human or not? It sounds like, smells like, feels like a human and even dies like a human. Even if you don't believe it that it was a human (or at least tell yourself repeatedly it wasn't) does it make a difference there if you think it was a human or not? (to me the "it was not a human" justification sounds like a few examples in the old wod for how characters justified things on a successful humanity roll)
Probably depends a lot on the Storyteller, but my take is that doing something for a good reason is irrelevant to the subject of losing Humanity. The "impassioned" vs. "premeditated" thing is really about whether you made a decision to do it or if it was an accident/physically unavoidable. There's no "pre-emptive self defense" here.
So your example sounds premeditated to me...the horrible things the cultists are doing doesn't mean you don't lose Humanity, it means you've decided that losing Humanity is a price you're willing to pay.