IMO, skunks are a huge threat because of the rabies issues. I would kill them because of that, not for the sake of my chickens, but for the sake of my children.
I am a huge animal lover, I even sympathize with the hawks that have taken a few of my chickens, they are doing what Nature intended. The only predators I have issues with are humans and stray dogs (again, human error). Skunks are dangerous, albeit cute - but deadly, to us. period.