Sometimes when you shoot a scorpion with a shotgun or when an explosion is next to it, the scorpion will flip over. You can run up to it and do a special knife kill. Sometimes when the scorpion jumps on you and you have to press a series of buttons to get it off, you will stab it in the head.
At the beginning of the level where you first see scorpions, you should have a shotgun and chaingun to go with the knife and bow. Unlike dinosaurs, scorpions are afraid of flares from the shotgun instead of being attracted to them. When you are trying to get to the chopper across from the lab, start by getting to the ground and setting up the auto-turret feature on the chaingun to cover you while you get to the ladder on the building on the other side of the open space. After you get on top of the building, you can see the short remaining path to the helicopter. Shoot a flare down to the ground and the scorpions should back away from it. If you stand next to the flare the scorpions will not attack you. Only the ones that appear from underground or behind you will not see the flare. Create a path with the flares and slowly make your way the chopper to end the level.