Oh goodness, I was horrified reading this. Picking up by the scruff is a terrible idea, they can kick and break their backs quite easily. The only time it's acceptable to "scruff" a rabbit is for medical care and they're on a flat surface as a restraint method (because then they're on the floor or a table, and they can't kick.)
We are as gods to the beasts of the fields. We order the time o' their birth and the time o' their death. Between times, we ha' a duty. - Terry Pratchett.
"Men have forgotten this truth", said the fox, "But you must not forget it. You become responsible, forever, for what you have tamed. - Antoine de Saint-Exupéry