The list of people that TSO's can exempt from selectee screening has changed a number of times. As it stands, in most cases the airline has the authority to exempt someone, not the TSOs at the checkpoint. In most cases if the airline makes someone a selectee the TSOs must screen them as such, or send them back to the airline to seek an exemption. Bottom line -- it was the airline's choice, not the TSOs

Since the rules for exempting people have changed a number of times and you haven't given any specific information I can't speak to this particular situation. I would bet though, that the TSOs would have exempted those Marines if they could have. This assumes that your talking about selectee screening when you say "secondary screening." Anyone that sets off an alarm will be screened, period.

As for your idealistic view of service members, as a veteran I can tell you that I knew more criminals when I was in the Military than I have since I got out. Considering the number of people I've seen court marshalled I think it's naive to assume that someone wearing a U.S. military uniform has no bad intentions.