For the same reason its permissible to shoot anyone attempting to attack and overpower you while you are carrying a firearm. You know, what they tried to hype up with their infamous jog-in-boots with his hammer and his drive-by building inspection and architectural analysis abilities.

But more far so, trying to rob a gun store raises the stakes dramatically if the robbers are not stopped with force, so preventing them from doing so must be just as important in proportion. Which means using force that would normally be excessive or overwhelming.