I've found that the key to keep them from scratching is to hug them to you like a football with their head tucked into your elbow.
I have always picked mine up by the scruff over their shoulders and never seem to cause them any discomfort or cause a problem with their skin. As soon as I get them lifted
enough though I do get a second hand under their rump.
My rabbits hate hanging out in open air.
When you go to put them down, hook your fingers behind their back legs and fold their legs back into their bellies. This seems to make them feel more secure and less likely to kick out.
Even so, I try to wear long sleeves and gloves if I know I'm going to be handling them.