Tame them. They're [PET_EXOTIC] but there is no dungeon master, so [PET] them and continue.
Alternatively, you could use the floating cage trick and some creative hatches. Place a hatch above the pit, as the only entrance. No stairs. Directly above this, build a wall. Directly atop this wall, build a cage trap. Link to lever, remove the supporting wall, and the cage will float. Pull the lever on the cage, the cage and mechanism pop out on the nearby floor, while the critter falls 2 levels onto the hatch. Then, pull the lever on the hatch, so the scorp falls 1 level into the pit. This would ideally be an "access pit" that has a short hallway into the main pit. Something like...
Side View:
L CW W
WWWW W
WHW W
W_____W
The W under the C should be deconstructed to allow floating. Prisoners fall in on the right, scorpions and other nasty critters are loaded from the left.
EDIT: If the floating cage is too hax for you, you can add a door between the L and C, and deconstruct the wall so that the scorpion, cage, and mechanism fall into the pit, but then you lose cages and stuff, and if you're on a desert those cages are expensive. You -could- add more stuff in the pit, like an airlock system that lets creatures leave the loading zone but not go back in, but it gets increasingly complicated from there.