Good question..a real toughie, but I think I would have shot him in the leg or buttock. Therefore disbabling the geek whilst keeping my hands free from blood. Juliet being a doctor of-sorts would be able to patch him up. Not sure I could bring myself to shoot Charlotte, she's growing on me..Ben would understand
Seriously tho, I'd follow Ben's orders through..I trust him more than Widmore and his band of pirates!