I capped the crucifixions at Nipton, it seemed the right thing to do at the time, still does.
I don't see the point in killing coyotes at all...they're pretty harmless. Anything that they are hanging around is pretty much useless to me anyway...I've either got tons of it already, or I could buy it.
There's enough 'grey shades' in the game to feel bad about without having to go looking for it on my own.
I always find it amusing how pragmatic people's sense of morality is in this game: It's wrong to get karma from killing someone, but it's okay to loot their body afterwards....
That's morality with a price limit....