I doubt I would have, but I wouldn't blame someone who did. If the guy just whips his hand back up a little faster than you can react, or turns around a minute or two after leaving and fires through the door, or comes back a day later (assuming he isn't arrested quickly), he could still kill you. If you kill him right then and there, any problems the two of you might have any time in the future are over. It seems harsh, but the second someone tries something like that I don't care about them anymore.
The store clerk handled that like a pro though. Apparently the whole thing didn't even really faze him that much. He made the superior moral decision ultimately in addition to being a total badass in the moment. Kudos to him.