I have had the same thing happen to me during deployments. We would pull the bolts from our weapons, tag them, and place them in a locked ammo can that we would carry on board. When we got where we were going, we would all pop our bolts back in once we cleared the tarmac.
I remember ONE flight where we were told in advance to place our knifes into our c-bags (checked bags) due to FAA regs.
I think that any time the military uses a commercial jetliner for one of its deployments it is subject to the same FAA regulations as a normal flight.