Drunkside, simply because you do not mind being essentially strip-searched doesn't mean that everyone else feels quite so free. Perhaps they do not have the bodies of greek gods to show off, or perhaps they might have medical problems that would be revealed by a scan. It really doesn't matter why. And simply because it has the misfortune of being routine does not make it any less offensive.
The question is, is using this machine as a routine security measure justifiable in the case of this man, who is to all accounts and purposes a known agent with a history with the airline? There was no reason to expect him to be hiding something which necessitates the use of a backscatter xray machine. Why should he be subjected to it if it isn't justified by his history, his bearing, his station, his character, his associations, the previous security measures he'd already been through or, well anything at all besides terrorism hysteria and it being "routine"?
Basically this situation strikes me like this: would it be reasonable to strip search your good friend on the off chance he's gone crazy and is packing a knife to stab you with since you saw him last week?