A neighbor of mine got prosecuted for shooting a skunk in his corn crib. I use a have-a heart trap, those kind that don't injure the animal. I then load it into my truck bed, drive a few miles from home, shoot it dead and toss it on the road like a car hit it. Coons too! As long as skunks can't raise their tail they won't spray.
I would bet the skunks smell after you shoot them though. I've heard that a person can use cat food in live traps as bait for skunks. Hey, if you could design a bigger trap to catch cougars you would make a fortune!