As long as you have secure housing for your birds at night then your best course of action is to leave it alone. Skunks can be trapped and moved without spraying by covering your trap with a tarp and moving them slowly and carefully (Skunks hate their smell too, and won't spray in a confined area generally.), but why bother? They are a nuisance, but they are not overly ambitious and will not actively seek out to harm your birds. They are opportunists that are probably attracted to your feed, so removing your feed from the run at night and minimizing wastage is generally enough to discourage them from hanging around too closely. I had skunks living around us for years with no losses. I became concerned about them last year when they moved in under my deck, but a motion sensing spotlight trained on their den was enough to get them to move on in less than a week. They also tend to discourage more persistent predators from residing in the same area as them because nobody can stand the smell of skunks, including predators. I looked at them as part of the natural defense system I have cultivated over the years.
