Where is that antelope chewing the popcorn thingy when I need it? Haha....
Seriously though, if you know a trapper, ask him about acetone injections. I think that is pretty common for non target catches of skunks. Syringe on a stick kind of thing...Never done it myself, but I hear it works well..
http://www.fntpost.com/Categories/Trapping/Odds+Ends/Syringes/do a google search for trapperman and skunk dispatch...