Keys and cell phones are also normally kept in pockets.
I was just about to say the same thing. Try explaining yourself when you're asked why you shot the guy...
"He flipped a desk over and put his hands in his pockets with a really mean look in his eye!"
I agree it's cause for alarm, but as it turns out a 911 call and some diligence paid off and in that case I don't believe I would have done much more. If he attempted to harm someone without any weapon I would have likely thrown a desk at his head.
Shooting someone in defense of myself or others is something I have no problem with and would not hesitate to do if necessary. It is a LAST RESORT. Take a look at escalation of force procedures and either match their hostility or one up them - don't just go straight for the gun... That is NOT what it's for.