Have you considered making your Captain of the Guard a very weak dwarf and assigning him a training sword?
Dwarves use their fists to hand out beatings now, so the weapon is irrelevant.
If you want to get the punishments cleared, either build enough prison space for everybody or make enough helms and mail shirts for everybody.
For the prison space, you can have three large rooms stacked on each other, with a stair between them available for each chain. One room gets the chains, another gets a food stockpile, and the last one gets a drink stockpile. The best time to activate this industrial prison is right after you've finished the hauling for the dwarven caravan. You can shut up the fortress over the winter, and right past the elven caravan if you still have too many dwarves locked up. If your dwarves are reasonably happy, you can get away with letting them eat off the stockpiles and sleep on the floor for a bit. You could also install a mist generator -- a square of four pumps might just about cover the 10x10 space you'll need for the prison.
For the mass beatings, you need a helm and mail shirt at minimum, to protect the skull and spinal cord. If you have any miners, woodcutters, or hunters on the beating list, don't forget to disable the relevant civilian labour first.