Crate Training 9wk old Puppy.?

My 9wk old mini dachshund puppy recently got introduced to the crate. She hated it when I first brought it to her attention, but I put a trail of treats into the crate and since then she has been going in on her own and laying down. I praise her and give her treats when she does go in and continually for a long period of time. She now goes in and the Vet told me to close to front to get her to like the crate. So today I did, she hasn't stopped whining and crying and chewing on the cage since I put her in there. I want to let her out so bad, first because she sounds horrible, and two because it seems so cruel. But she went in on her own terms I just closed the door. HELP WHAT DO I DO? Do I take her out or do I leave her in there and hopefully the whining and crying will subside? I don't want her to hate the crate because of all of this whining. I don't know what to do, they say let her whine, but it sounds horrible.