Yes sounds like your puppy has a bit of separation anxiety, is he still very young? I can relate to feeling guilty, when we first started leaving our puppy alone he would cry like something was crushing him, but it doesnt last forever, once they learn the routine.
I also wasnt sure about using a create but, to him that is now his safe place, even though now we leave the door open he will not sleep at night if his bed is not there
. I also used the bach flower remedies with him for a while to help him with his anxiety/fear with great results too. Also, both of my dogs are very small, so I always leave training pads for them, because you just never know, if we are running late or something happens and dont make it home right on time to let them out they can have another option, since their bladder is so small.