CIA doesn't really operate within US soil and it doesn't target US citizens. Most of the missions shown in this series would have been handled by other agencies.
General Diane Beckman works for NSA but she often assigns missions to Sarah and Chuck who work for CIA which is a completely different agency. CIA agents wouldn't get orders from NSA officers.
During the intro of every episode, the gun visibly fires a cartridge, complete with case/shell, instead of just dispensing a bullet.