Although slightly intimidating at first, once used to using a whip finishing tool, i feel its the only way to go. After using it on a couple flies, its second nature. I watched a video on utube showing how to use it, very helpful.
All my flies seem to be very durable using the whip finish, it's also more accurate when tying off small flies. I use the whip finish and then add a coat of "hard as nails" clear polish to all my fly heads.