In pure honesty, I really believe crates act more like band-aids than training aids when dealing with SA. I speak from experience only so your pup might be different, but, in my experience, dogs with SA tend to react more when confined to a crate. It might not be the case with your pup, but being confined to a small space when all you want is OUT can result in a mangled crate and a possibly injured pup =/

Obviously, exercising isn't an option now but once he recovers from the treatment, I'm sure things will get better In the meantime, how about mental exercise? You could try teaching him to retrieve certain objects. I knew a Dane who knew how to differentiate objects by name and retrieved them for his owner. It's a greyt way to work their brains!