As far as we know, nobody knew that the FBI were involved in Kir case except for Vermouth, who saw Jodie and Conan in Haido park where the assassination was supposed to take place. Given the fact that Vermouth,usually hides Conan-related information from the boss, she wouldn't have reported to the boss that the FBI are involved. Plus, even if the boss knew that Akai might show up, He/she would have planned some way to kill Akai since he/she believes that he is the silver bullet. Waiting for his/her own enemy, Akai, to save their guy, Kogoro, that the boss gave permission to kill.and put his highly ranked agents in a dangerous situation, doesn't make much sense in my opinion.