Caged prisoners are docile and can usually be hauled places with no repercussions. I like to designate a death pit that my archers overlook - just a 1 zlevel pit with a sealed door/floodgate and a stationed archer squad above it. Assign a pit area, assign the gobbo to be chucked into the pit and once he's in the squads turn him into a pincusion.
Of course just a deep death pit with nothing special can also be used, or a pit over a volcano for live sacrifices to the magma god, or something. You can also build a cage with a gobbo in it and set it to a lever - when the level is pulled, they'll be released, in case you'd like a time-delay system. Or, if you're feeling like making an actual jail for prisoners of war, you can build a chain and assign them to it. Be warned - all caged prisoners, if they get free of their bonds and aren't being handled by a dwarf, will immediately attempt to run away from the fortress causing cancellation spam as the streak through the dining room. If they don't have their equipment, they're generally not deadly - barring lucky punches to the head if a dwarf engages them for whatever reason - but it's a waste of valuable military experience if they get away.
As for the thread - turn off brewing for pig tails. Dwarven ale is tasty, but it doesn't give the fortress tantrum-reducing pants. Make sure you've got pig tails in your stockpiles too before trying a processing job. If you need some immediately, designate some Gather Plant jobs in the caverns - pig tails should be in there somewhere.
Remember, only rope reeds and pig tails are processed into thread, so if you want plant-based cloth you need seeds of those crops to grow (pig tails only grow during summer and fall).