Then why would the guy jump him after he shot and killed the other? he should have run or assumed the begging position.
It sounded as though it went down like this:
Store owner sees suspicious activity at the store and investigates. He has a gun in his pocket but does not draw it. The robber with the shotgun gets the drop on him and orders him to his knees.
The other robber hearing the first call to him, comes to investigate. At this point the store owner, fearing he is to be executed, slaps aside the shotgun as he rises, struggling with the first robber. He manages to draw his pistol and shoot the robber he is struggling with, mortally wounding him. As this is going on, for perhaps two seconds, the second robber reaches the struggling pair as the first robber is shot. He is committed, so he continues the attack, but the store owner now has his pistol in his hand and is able to shoot and wound him and drive him off, in the next two seconds.
Total elapsed time from the decision to resist - maybe 4 seconds.