Despite the drek you see on the pirate trids, "shoot first, then question the remains" isn’t Lone Star SOP, and ambushes aren’t just another assignment. The FRT team leader would almost certainly have questioned the order, and checked it out through various channels. Unfortunately, those "various channels" would all have been electronic and computer-mediated, and IrreleCorp could have given the correct verifications and authorizations to set the team leader’s little mind at ease that the op was kosher. Off lumber the armed and armored troopers to do their bit to save Seattle.