I had the same woes as you recently. Together with other Bay Watchers, we developed the following solution. It was made to dispose of prisoners, while keeping their gear available for looting, and while keeping the cages available to be used again.
DWARVEN DEATH PIT (MINIMAL VERSION)- Prepare a chamber. It must be 5x5 tiles, and 2 Z-levels high. The floor of the upper Z-level must have been dug out. This'll be the Death Room.
- Above the chamber, prepare a room of any size (3x3 minimum). We'll call it the Prep Room.
- In the middle of the Prep Room, channel one tile, build a hatch cover onto the hole, and forbid it.
- Around that hatch cover, put an animal stockpile that's 3x3 tiles, this way every space of the stockpile touches the hatch cover from any direction.
- Setup another animal stockpile elsewhere, and set it to Give To Pile, specifically to the stockpile in the Prep Room. Make sure to set up a lockable entry point to the animal stockpile there, as you want your dwarves to be forced to use the Prep Room stockpile in specific circumstances. More on that further below.
- Arm your Death Room with whatever you choose. Weapon traps are the ideal middle ground in terms of ease of setup, and maintenance. Take note however that some of your enemies might be able to dodge weapon tracks endlessly, thus forcing you to eventually open up the Death Room and have the militia finish off the stragglers. Magma is another option, but then again some rare foes can easily live submerged in magma.
With the above design, you can designate your foes for pitting. Lock the door to any other animal stockpiles (if you're like me and you select the entire list, then de-select whatever wasn't pitted afterwards.) Your dwarves will take your prisoners, and
somehow shove them through the forbidden hatch cover, down into the Death Room. Because some foes can climb, the Death Room was made large enough that enemies can't climb back up the hole, and high enough that they can't fight back from below. Enemy escapes are also made exceedingly rare, and only in the event that a dwarf somehow gets interrupted or attacked while trying to pit a creature.
DWARVEN DEATH PIT (ADVANCED VERSION)- Prepare a Prep Room and a Death Room much like you'd do above. However, this time, make the Death Room as large as you desire. The bigger the Death Room, the more quickly you'll be able to put your prisoners.
- Your Prep Room will contain several zones, each of 5x5 size. Each zone will have one hole with a forbidden hatch cover, surrounded by an animal stockpile, and thus there will be at least a tile's width of space between each drop-zone if you will. Make just one big animal stockpile, and then remove pieces of it until you're left with the desired layout.
With this design, you can pit enemies much more efficiently, by the dozens instead of only by the eights. Making the Prep Room large enough may even remove the need for a giver stockpile.
THAT SAID!Considering how cumbersome mass-disposal maneuvers have become lately, I recommend a more expeditive approach: a glorious battle between your militia and the invading force! If your dwarves are well-trained and numerous enough, they'll be able to take on a full-sized siege with but the occasional loss every few years or so. I suggest this approach if your focus shifts towards managing other areas of the fort.