Drowning is cruel. I've found that putting the muzzle of a .22 rifle thru a gap in the have-a-heart cage, will almost always prompt the animal to come sniff the barrel. One clean shot thru the head, instant death, and usually no damage to the trap.
I've disposed of quite a few ground hogs this way, as they're both illegal to relocate, and can tend to come back if not moved farther than 3 miles. If I had a skunk that needed to be gone, I'd surely use the same method. But I like skunks, as long as I can keep my dog and them separated, they keep German yellow jacket (aka "ground hornet") nests at bay.