Crate training in not only not cruel it is kind.
A dog left on it’s own will seek a secluded space to sleep. A crate with the door open gives the dog 3 walls and a ceiling of security.
We always had the open crates in our bedroom and the dogs would choose where they would sleep at any given time; beside the bed, in the crate, by the door or wherever.
I always felt quite secure with that arrangement.
Pretty much too late for the OP though, unfortunately.
They like a den.
And it keeps them true to who they are.
It’s NEVER too late.
I have successfully rehabilitated Dobermanns that were well into their middle/senior years.
A crate is an -excellent- idea...especially until the blood work comes back.