Is it ok to just let a puppy scratch in his crate?

Ok before anyone starts giving me the knee-jerk advice: YES he gets exercise 2-3x a day. He also has been given praise and treats while in the crate. He has never been in there for more than a few hours either. This is a 5 month old male Maltese by the way. So anyway my question is: is it OK like at 5am when I'm at my wits end to just let him scratch, bite the wires, bark and in general FREAK out? wont hel eventually learn it gets him nowhere if I don't say anything, look at him or let him out? He seems to have quieted down and even stopped the hyperventilated breathing... but it's like I can't tie him up ever anywhere either or he barks his head off. He's such a sweet little guy I know he just wants his pack together all the time but he cant be trusted to hold it through the night. so to refine my question: do I respond at all? or suffer the 15-20 minutes of him going ape **** THEN say some soothing words?