If you can kill them temporarily, you can always designate-dump them into a pit they can't get out from (assuming they can't fly. Can undead fly?) Bonus Bio-Hazmat-Team points if the bottom of the pit is on fire or filled with magma.
However, from the sound of it, you don't have many dwarves to spare. So, you'll need some kind of unmanned solution. Working on the assumption that the undead don't dodge (rendering dodge-drops useless) I instead propose a ridiculous bridge flinging solution:
Dig a big pit, long enough to require 3 bridges across and maybe 1 or two tiles wide. On one side, provide an entrance from the surface. On the opposite side, provide bait, (an animal if you have one, or a dwarf if not.) The all 3 bridges should have an open square above and to both sides, as well as be centered over the pit. The bait-side should be 3 tiles long, with the bait on the furthest side and a 2 square bridge oriented identically to the first 3 bridges. The bait-side room should be constructed such that when it's bridge draws up, it creates a solid wall separating the room from the rest of the bridges (sealing off the bait-space in case of problems.) The bridges should all be linked to draw up together and away from the bait-side. Finally, a lever is placed where the operator will not be startled by the undead. Lock a dwarf in the lever space with only a repeated task of pull that lever. Let the undead in and watch them be flung into the pit. Spikes optional.