Crate them. I know how you feel. Archie joined us a little over a year ago at 5 years old and he is still crated at times. He scared the dickens out of me one time by eating almost an entire box. He did not tear it up, he ate it. Was so worried about an obstruction.
Your pups will be OK. They think of it as their safe place, their den. And it is a safe place for your house and for them; they could get into some serious trouble causing themselves injury. Don't feel bad about it, you are protecting them. Given adequate exercise, physical and mental, during the times they are out, they will be just fine.