Before I say anything dumb, I was wondering what your MOS was.
Secondly, having had a short career in Marine Corps Aviation, specifically ordnance, I can tell you EXACTLY what the paper trail may (or may not) be in place for military hardware. Just curious.
EDIT: Though I would entertain a conspiracy theory if it had at least a bit of merit, the chain of custody that an ordnance officer follows is insanely rigid. Not a chance in hell that a sortie came back with an empty launch rail and an unaccounted for weapon. Never happened, never could happen.
Also if a shoot down order were carried out, there'd already be about a dozen or more personnel aware of it before the pilot toggled step-reset and pickle. WAY too many people to hush it up.