If, and I mean IF you or the clerk are in danger of being shot, take him out. But if he is just stealing the money, does NOT point the gun at you then hide and call 911. You don't get paid to be a hero, and the store has insurance for the theft.
Just to give you a "for instance": you are standing there, and he pulls a gun at the clerk, you put a cap in his a@@ and it turns out he had a water gun, YOU ARE SCREWED.
There are many different opinions on this here on the board and someone will come along and tell you to put a cap in him, but in a split second you have to make the decision that you will have to live with the rest of your life.
Now that being said, if I'm standing there and some guy runs in a robs the place and starts shooting, say into the ceiling, I can't be certain the next round will not be in the clerk or myself, or anyone else standing (or at this time hiding) I would have to think that I would be able to take the shot to save a life. But if he is just waving a gun around then no I would not be able to justify it in my own mind.