aw he is such a sweetie!
Do you normally leave him in the create when you are out? I personally wouldn't use the create as a punishment, because he will now relate that as a place where you go when you have done something wrong, so if you leave them during the day when you are at work or something, he may think he has been a real bad boy; and not really see the crate as a safe place, his home per say...
when our puppy has been bad we just give him a little "time out", and its funny because he actually sits on the spot and waits until we say OK come back