Actually, I have denied the jumpseat to an FAA inspector. Aside from having to file an Irregular Operations Report, I heard nothing more about it from either my company or the FAA. In fact, the FAA inspector was very understanding when I explained why I was denying the jumpseat. He nodded, said thank you, and walked off of the airplane.
Maybe I was just lucky?
Kind'a hard to say how lucky you were without knowing the reason for the denial. I suspect you had a valid safety reason, ran into a very nice Inspector, or the Inspector had enough on his plate and didn't want the hassle of more paperwork. The policy used to be that denying the JS to an Inspector for other than a valid safety reason meant an emergency order suspending your ATP would be waiting at the next scheduled stop. That might have recently changed, but I doubt it. The reg is pretty clear and doesn't have a lot of wiggle room except that 121.547 makes it clear that the PIC can exclude anyone from the flight deck for reasons of safety.
§ 121.548 Aviation safety inspector's credentials: Admission to pilot's compartment.
Whenever, in performing the duties of conducting an inspection, an inspector of the Federal Aviation Administration presents form FAA 110A, “Aviation Safety Inspector's Credential,” to the pilot in command of an aircraft operated by a certificate holder, the inspector must be given free and uninterrupted access to the pilot's compartment of that aircraft.
