Tower sieges often bring undead armed with weapons and armor. While all undead have massive boosts to their physical stats, most die (loose all equipment) then get resurrected naked. This makes them fairly harmless... but Thralls (and Tower sieges) still contain equipment AND their mad stat boosts to str and toughness. As you noticed, a lone undead with some equipment can just tear through your military.
Like all things dorf, I recommend immediate application of magma with -extreme- prejudice! Magma is the solution (and often cause) of all dorf-kind's problems! If you don't want to fool with magma, try making a collapsing tunnel that drops 25z levels. This should be a long enough drop to explode anything upon hitting the ground. Don't care how tough they are, 250 foot drop onto stone will turn them into zombie-mash. I suppose spear and spiked ball traps could work too. A note on weapon traps- the quality of the mechanism impacts the attack rolls of the 10 weapons inside. So only use your highest-quality mechanisms for them (in comparison, cage traps ignore mechanism quality for functionality).
Speaking of cave-traps, if the bastard wasn't trap-avoid before zombiefication they won't be afterwards. I hate to say it, but if you had used 50 cage traps instead of 50 (worthless) stone traps, your siege would have been over already. Of special !!FUN!! is to at least capture a necromancer or two and use them to train soldiers. Set them up in a fortification carved/bridge blocked (for controllable line of sight) room. Create a (small) corpse stockpile on the other side of the bridge. They'll constantly kill the zombies while the necromancer reanimates the corpses for more creatures to kill. When things get out of hand/you wnat to stop, raise the bridge to stop the pieces from being reanimated. Thus, you can give your dwarves live training while giving your Doc practice that doesn't involve meeting rooms set up over bridges. So long as the zombies lack equipment (or are simple beasts) and your dwarves outnumber them, there shouldn't be much risk of death.